As I said, Obsidimen have natural armor. That is in addition to equipped armor. The question is, since they effectively have two armor and if Spot Armor Flaw is against the armor, can you use Spot Armor Flaw twice on the same Namegiver. Providing an example of how it can effectively be used once against their equipped armor doesn't really address the question.
A big crux of the problem is "what is being targeted?" I'd argue the armor is being targeted, both given the name of the Talent and the fact that a higher armor MD overrides the Namegiver's MD (which is likely to happen, given low MD of most fight-y guys compared to Thread Item armor MD). Since the armor is the target, and not the Namegiver, the "a target cannot have more than one instance of an ability applied" doesn't count, you could do it twice: once on the Obsidiman's equipped armor, once on the Obsidiman's natural armor. The end result is that you'd get the benefit of Spot Armor Flaw twice on that Obsidiman.
Side note: There *used to be* a note *somewhere* that said "you cannot use Spot Armor Flaw against a creature without armor." I've long since forgotten where that was. Also, I can't remember if that was "without" or "not wearing," the latter being of the utmost important because one does not "wear" natural armor. Regardless, you obviously can't Spot Armor Flaw on, say, a Dwarf without armor (to include Blood Pebble), but if Spot Armor Flaw works on natural armor, than you can *ALWAYS* use Spot Armor Flaw against Obsidimen, even if they're buck nekkid.
I also have this vague recollection of something saying "you cannot use Spot Armor Flaw if you cannot see the armor," which makes total sense - kinda hard to spot a flaw when you can't see the armor. Usually, this isn't important, but there occasions where it could be, especially magicians (given their penchant for robes, pretty easy for a robe to cover almost every type of armor).