The Ioun Stone comes from Jack Vance's Dying Earth series, which is where the "fire and forget" spell casting of D&D came from too, as well as some of the spells such as prismatic spray. The stones are harvested from the core of neutron stars that are being sliced away by the Nothing at the edge of the universe and are therefore rare and difficult to obtain. Their origin is dealt with in the story "Morreion" in the collection Rhialto the Marvelous.
They were introduced in The Strategic Review, Vol. 1, No. 4, p. 10 (Winter 1975; no author given, although there is a reference to Vance approving the design/inclusion and I know he and Gygax corresponded) and first made their way into the rulebooks with the original DMG, as far as I can see.
By strict RAW, it would seem that the ioun stone grants all the benefits of the ring, except with a lower healing rate.
This stone grants the wearer the ability to regenerate 1 point of damage per 10 minutes. Regeneration works like a ring of regeneration. It only cures damage taken while the character is using the stone.
Contextually, "works like a ring of regeneration", with no colon- or dash-separated clause to restrict it, does in fact include everything. The following sentence restates the key limitation for clarity and rephrases it to apply to the stone instead of the original ring (which wouldn't make any sense).
While the normal rationale for the immunity to bleeding damage that the ring gives can be thought of as a logical outcome of the constant healing, it's given as its own feature, so it applies without regard for order of operations or any other exceptions: the wearer is not merely cured of any bleeding at the start of each turn, but cannot take any damage from that. As such, it still applies the same way to the ioun stone, even though the stone does not heal nearly as often. (This can be justified in fluff as simply being such a slow constant healing that it only adds up to a single point every ten minutes, but in any case the RAW seems clear enough.)
From a standpoint of balance, which is certainly not a standpoint of RAW but can at least inform houserules, the ioun stone's additional abilities are not nearly so imbalanced as one might think. Bleed damage is not unheard of, but neither is it all that common, and limb removal does not, as far as I know, actually have any rules to enable it. So charging 20,000gp instead of 90,000gp for 1/100 the healing rate isn't too cheap. If anything, it's really not that great a bargain, and the original ring cost a pretty penny anyway.
Best Answer
from the same page you linked:
Emphasis mine. So, simply using a stone that already has a crack in it as the crafting material would automatically make the end result a cracked Ioun Stone. If this is about lowering the cost of the crafting process, I am pretty sure the DM would allow you to simply buy a pre-cracked stone at a lower price - since this makes up a good portion of the crafting cost, you'd already save some money.
I am guessing that "whether as a result of the crafting process..." refers to getting a subpar result on the crafting check. IIRC, if you manage to make a check's DC with your crafting skill and roll, you can always choose to have the result of your check be lower than what you rolled, since that purposefully makes the item you create work worse than it should by your roll. I think you are also allowed to just forego the roll entirely and just take the result your skill bonus gives you in case of crafting - if you can make the DC regardless, because your skill bonus is high enough, some DMs actually allow this to speed up the game. And if your skill bonus just barely misses the DC, the DM might tell you that you actually cracked the stone while crafting, but still managed to craft it.
In any case, these suggestions are not exactly RAW. The exact process for crafting your Ioun Stone is up to your DM - the RAW are purposefully vague on this, because they want to promote creativity, since crafting powerful items may even become an entire sub- or sidequest, sending you on a hunt for rare materials - but I think you should be able to purposefully craft a cracked Ioun Stone. It would require asking the DM in any case, maybe he even allows you to lower the DC of the craft check to make a cracked stone, but there are no exact rules on that in the RAW, mind you.