Nice theoretical question. :) And I partially disagree with the other two (?) answers (that I've seen so far.)
I'd say you could place the Bag of Holding around the Immovable Rod, or push the Rod into the Bag, though with a very, very serious effort -- a DC 30 Strength check -- only. Why? Because
"the rod does not move from where it is", ie. it has a pretty fixed position in space, and
"The bag of holding opens into a nondimensional space", that is, the inside of the bag is a different place,
...and the rod does not move from where it is, unless you apply serious force (a DC30 STR check, as per the rules.) Pulling the bag over the rod or pushing the Rod into the Bag would cause the Rod to move, from the original dimension to the bag's dimension. It would be like trying to touch two similar magnetic poles to each other - which can be done with great enough force. So, you could pull the Bag over the Rod, etc... with a DC30 STR check.
If you activate the Rod within the bag, its position will get fixed within the Bag's "nondimensional" space (whatever that means) only, so you'll be able to move the Bag anywhere on the outside, with the Rod in a fixed position in it.
In case you activate the Rod when it's only partially covered by the Bag, moving the Bag off the Rod, or moving the Rod along with the Bag would be a DC30 STR check, since the Rod would have a fixed position both within and without the bag. (Well, depending on your view of physics and magic, you could lower the DC in such a case to your heart's content.)
From the d20pfsrd.com entry:
If living creatures are placed within the bag, they can survive for up to 10 minutes, after which time they suffocate.
If you can suffocate in the bag, it is air tight. If it is air tight, it must be water tight. (Though, presumably, both of these conditions are incumbent upon the bag being closed.)
Best Answer
There is no perfect storage
Any time a creature uses an item for storage, that item will be vulnerable to destruction and loss. However, in my experience, folks—that is, PCs and NPCs—are first satisfied by a Heward's handy haversack (Dungeon Master's Guide 259) (2,000 gp; 5 lbs.) then by an enveloping pit (Magic Item Compendium 159) (3,600 gp; 0 lbs.) or six, despite these items' vulnerabilities and the possibility of losing them. These have been the go-to options over multiple campaigns that made it to the late teens with experienced players. Higher-powered storage just wasn't typically necessary. (And, when it was—for, like, important corpses and stuff—the PCs would leave whatever it was in the hands of an NPC who was either oblivious or in a fortress.)
I bring this up not to minimize your concern! My opinion as a DM is that NPCs generally don't seek to destroy PCs' stuff but to destroy the PCs and take the PCs' stuff, just like the PCs do. A DM that doesn't share this opinion may go so far as to have roaming bands of invisible knife-wielding kobolds that, for kicks, slash any sack dangling from an adventurer's belt. If the DM's running a campaign like that (probably to a lesser degree, obviously) then it may be wise to just ask, either in character or out of character, "How does a guy keep his stuff safe around here?" Have the DM (or an NPC) tell you (or your PC) the DM's expectations (i.e. how to keep your stuff safe).
Nonetheless, below are some storage ideas, assessed in light of the question.
Magic items that are extradimensional storage spaces
A bag of holding (DMG 248) (2,500+ gp; 15+ lbs.) is particularly vulnerable to destruction because "[i]f the bag is overloaded, or if sharp objects pierce it (from inside or outside), the bag ruptures and is ruined." To be clear, that means "[a]ll contents are lost forever." And, sadly, this vulnerability extends to everything that's like a bag of holding, from a belt of many pouches (Complete Arcane 147–8) (11,000 gp; 1 lb.) to a druid's satchel (Dungeon #92 103) (3,000 gp; 5 lbs.) to a Heward's handy haversack (DMG 259) (2,000 gp; 5 lbs.) to a nondimensional trunk (Arms and Equipment Guide 50) (30,000 gp; 200 lbs.) (steamer not elephant).
For the question's purposes, the best of these may be the belt of hidden pouches (Races of the Wild 173) (5,000 gp; 1 lb.) because at least it's concealed. Its capacity is comparably insignificant, though.
A portable hole (DMG 264) (20,000 gp; 0 lbs.) or its cheaper and deeper brother the enveloping pit (Magic Item Compendium 159) (3,600 gp; 0 lbs.) can be folded into a pocket square, but retrieving anything from it can be a woeful exercise, taking far longer than you want.
One spell and one class feature that are extradimensional storage spaces
The 1st-level Sor/Wiz spell hoard gullet [trans] (Dragon Magic 68) puts items the caster swallows into an extradimensional space, but the only way to retrieve anything from that extradimensional space is by barfing forth all of the items in extradimensional space, making it awesome but still impractical. The nomad alternative class feature personal space provides a more readily accessible internal storage area, but it doesn't hold much unless one is a high level nomad. (Also see this question.)
(War Story: I DMed Castle Amber converted to 3.5. The adventure frequently features thousands in coins as treasure… often in silver. Because exiting Castle Amber was impossible, and the party entered with no extradimensional containers, upon leveling up during the adventure the party wizard picked as a spell to add to his spellbook the hoard gullet spell and used it constantly on himself and his familiars so that the party could tote around their wealth.)
The problem with having your own demiplane is getting there and back
A ready drink helm (Dragon #294 80-1) (150 gp; 2 lbs.) (also see this question) allows a dude to consume as a free action a potion of plane shift, arrive at the demiplane of storage (that's actually quite small—like a 10-ft. cube—so that the plane shift effect can't deposit him 5d% miles off target), take a move action to retrieve an item from the storage demiplane, and consume as a free action a potion of greater plane shift to return exactly whence he came, the whole process leaving the dude with, on his turn, still a standard action and a swift action to employ whatever he retrieved. This is incredibly convoluted… not to mention expensive. (A potion of plane shift [conj] (PH 262) (5th-level spell at caster level 9) (2,250 gp; 0.1 lbs.) and a potion of greater plane shift [conj] (SpC 159) (7th-level spell at caster level 13) (4,550 gp; 0.1 lbs.) can be created by the prestige class master alchemist (Magic of Faeûrun 34–5) at prestige class levels 3 and 7, respectively.)
It would be better to access a demiplane through a moving portal à la the feat Create Moving Portal (Perilous Gateways Web column “Portals of Anauroch: At’ar’s Portal Collection” available here). While carrying around a hula hoop of adamantine or something may also seem impractical, it'll generally be less vulnerable than a bag of holding. However, this option, too, will be extremely expensive and isn't available at the typical magic mart.
Shrinking items has its own problems… and a horrifying solution
Casting on important nonmagical items (or magic items that have been made temporarily nonmagical with a dispel magic effect) the 3rd-level Sor/Wiz spell shrink item [trans] (Player's Handbook 279) then the 5th-level Sor/Wiz spell permanency [univ] (PH 259–60) allows the caster to change the item from its original state into a square of cloth and back, but that's expensive, complicated, and requires being that caster or having a significant Use Magic Device skill modifier.
This DM once approved for use in one campaign a glove of the master strategist (Ghostwalk 71) (3,600 gp; 0 lbs.) to which was added a second glove of the master strategist (Ghostwalk 71) (3,600 +50% = 4,400 gp; 0 lbs.) for a PC that really needed to have two things always at the ready. (He'd snap twice.) The campaign survived without issue and everyone was happy, so that's a possibility. (The glove is a better and less expensive glove of storing (DMG 257) (10,000 gp; 0 lbs.), so you know.)
I was very close to suggesting straight-up the deeply obscure dragonskin bag of Grendel (Dragon #329 26) (18,000 gp; 8 lbs.) that's otherwise like a bag of holding (type IV) except it doesn't send items put into the bag to a demiplane but actually physically shrinks items put into the bag to 1/16 their normal size. (Creatures and magical effects won't go in.) However, the text notes, if a dispel magic effect is successfully used on the bag, the contents resume normal size, destroying the bag. Thus, in this player's opinion, the dragonskin bag is even more fragile than a bag of holding. (The bag's default caster level, by the way, is a mere 5.)
That solution? An embedded warforged component
Eberron Campaign Setting says on Warforged Components, in part, says
…Which is fine if you're a warforged, but what if you're not? In that case, for near-perfect storage, a nonwarforged creature could commission a wondrous item craftsman to create an embedded warforged component dragonskin bag of Grendel that has a market price of 36,000 gp. Then the creature could make a Use Magic Device skill check to emulate a race (DC 25) (also see this question) and, with success, for 1 hour, the embedded warforged component dragonskin bag of Grendel would function for that creature as if the creature were a warforged.
While its embedded, the embedded warforged component dragonskin bag of Grendel can't be targeted, isn't subject to vagaries of the random number generator, can't be stolen, and can't even be opened (i.e. activated) by anyone but the creature in whom it's embedded. And no pesky adventurers can use teleport or plane shift effects to visit the bag's interior. (The dragonskin bag won't let in creatures, remember?)
While this is a lot of resources to invest, I can't think of anywhere more secure that still meets the question's high standards. For example, while similar results can be had with the embedded warforged component camouflaged compartment (Dragon #352 80) (12,000 gp; 0 lbs.), the compartment remains an extradimensional space—therefore vulnerable because of it—, but it is not otherwise like a bag of holding, so it won't implode when the warforged (or ersatz warforged) enters its ally's enveloping pit. This would, I think, be the second safest—and perhaps less embarrassing—alternative to the embedded warforged component dragonskin bag of Grendel.