You're misusing the guidelines.
First, let's take a look at what the Pathfinder Magic Item Gold Piece Values section has to say on this issue. Turns out, it is specifically addressed.
The correct way to price an item is by comparing its abilities to similar items (see Magic Item Gold Piece Values), and only if there are no similar items should you use the pricing formulas to determine an approximate price for the item. If you discover a loophole that allows an item to have an ability for a much lower price than is given for a comparable item, the GM should require using the price of the item, as that is the standard cost for such an effect. Most of these loopholes stem from trying to get unlimited uses per day of a spell effect from the "command word" or "use-activated or continuous" lines of Table: Estimating Magic Item Gold Piece Values.
Emphasis mine. It then goes on to take Mage Armor as an example of this:
Patrick's wizard wants to create bracers with a continuous mage armor ability, granting the wearer a +4 armor bonus to AC. The formula indicates this would cost 2,000 gp (spell level 1, caster level 1). Jessica reminds him that bracers of armor +4 are priced at 16,000 gp and Patrick's bracers should have that price as well. Patrick agrees, and because he only has 2,000 gp to spend, he decides to spend 1,000 gp of that to craft bracers of armor +1 using the standard bracer prices.
So yes, your Amulet of Mage Armor and Shield is a textbook example of the guidelines gone bad.
This is understandable. The guidelines are famously weak, often breaking with casual use, as you have encountered. This precise case, however, was anticipated and addressed.
The Rules Don't Say
As nvoigt pointed out, the PHB describes chain mail and plate mail as complete items. They are either on, or they're off. There are rules for how long it takes to put them on and take them off, but there is no description for your AC while wearing just the padding.
Furthermore, the padding under plate and chainmail isn't padded armor. Padded armor is a different thing. When you buy plate mail you don't get plate mail armor that has padded armor inside, you get plate mail armor that has padding inside.
You Could Try It
Since there are no rules that describe this situation, you are down to the most general rule of all. At the beginning of the Players Handbook, it says:
1.The DM describes the environment. ... 2.The players describe what they want to do. ... 3.The DM narrates the results of the adventurers' actions. (PHB p.6, "How to Play")
So, your character could just try it and see what happens. "Try it" could mean a lot of things. "My character takes off all his armor but the padding. What's his AC?". "I'm looking at the swamp we're about to cross. I'm an experienced fighter, I've been wearing armor for years, I've been trained by experts. I know if I fall in wearing full plate, I'll probably drown before I can get out of it. What does my training tell me about whether I can wear just the padding in order to mitigate the drowning risk but still retain some protection?" Or perhaps your armor wearer might consult armor experts.
You've Solved My Drowning-in-Armor Puzzle!
As a GM, I view the water-armor situation as a challenge or problem for the PCs. Which do you do, take off the armor and carry it thereby lowering your AC, or wear it and risk drowning?
Only it isn't an either-or, which is the beauty of RPGs. There are other solutions to the problem. Perhaps the water is such and the PC's strength is such that the PC can just walk out, perhaps with a strength or constitution check. Perhaps the PCs have access to magic that allows them to breathe water. Maybe they can bypass the swamp. The players might (and hopefully will!) have innovative solutions I haven't thought of.
If the PC said, "I take off most of my armor, and wear only the padding", or "only the helmet, gauntlets, greaves and leg guards" and subsequently fell into the water I think the time to remove the armor and thus the risk of drowning would be less, while the chances of swimming in part of the armor would be more. And if the PC were attacked by Rodents of Unusual Size while crossing the swamp, I'd definitely have to allow that the PC's base AC in padding or other bits and pieces was greater than without armor. Wearing only part of the armor might be a reasonable solution to the but-I-might-drown problem. Although wearing only the padding might be really bad for it, given briars and such.
Given that I don't want to play "Armor & Anoxia" I'd be reluctant to come up with a codified houserule that says you can wear half the armor for half the AC and half the risk of drowning, but perhaps that would be the solution. I'd definitely want to keep things liquid, and not weigh the game down with heavy armor questions, but I'd definitely want to pad it enough to keep things moving forward, while at the same time rewarding innovative role-play and problem-solving.
Best Answer
Yes, animal companions can wear armor. It is usually called barding but the only difference is that armor for unusual creatures is more expensive.
As long as the armor has no armor check penalty the companion doesn't even need the proficiency.
That means masterwork studded leather can be worn by companions without proficiency.
One thing to note is:
I guess that would apply to other flying companions, too. It's from the section about barding for horses and the like directly above the armor for unusual creatures section I linked.