I'd considered this but we don't really have enough evidence to suggest anything more than transfiguration fixing. Hermiones body is transfigured by the dark lord, the stone is what sets it. She was trollified as a separate process prior to the fixing, but it is the transfiguration made permanent is what rendered the trollification permanent. It seems to be an indirect effect, it will preserve whatever qualities a transfigured object possesses. Basically it is an advanced application of the stone. As a culinary metaphor, the stone is like a refrigerator that allows the jello to set. You can mix any flavor you like into the jello, but it is the change in temperature that sets the flavor in place. You cannot mix a new flavor into already set jello; you need to melt it again because by mixing you simply destroy its structure.

This would make sense, if not for the actual sequence of events: body restoration>stone>clothes>patronus>trollification>stone>unicornification>stone>horcrux. The transfiguration was fixed before the trollification occurred, so the fixing of the initial transfiguration cannot be what set the trollification. LV didn't visibly transfigure her in the meantime, and since he'd have no apparent reason to conceal his doing so it's reasonable to presume that he didn't.

At least for now, I have to invoke Occam's Razor; the (mythical and known to be immensely powerful) Stone having more general magic-fixing powers which work on transfiguration seems to require far fewer and less complex assumptions than the alternative.

Cool! I hadn't considered this. Harry uses acid to fight the troll, at no point do any of the experienced wizards freak out about the smoke the acid creates. This is best argument against the troll regen transfiguration hypothesis. Does this mean we can start making troll burgers? Wizards have had the cure for world hunger for several millennium but are too silly to see it? The last bit I can believe.

Also, if troll regeneration were based in some sort of autotransfiguration we'd expect to see really weird reactions if someone tried to transfigure one into, say, a false tooth. It might still work, but it would likely have been remarked on at some point. This also applies to dead trolls, since if their mass is at least partly transfigured (it would have to be, if they'd had a body part grow back) that transfiguration would presumably expire relatively soon after their death. As far as troll burgers go, my guess would be that troll meat is either thoroughly poisonous to humans and other similar creatures, or disgusting enough that wizards (who don't seem to have issues with food scarcity anyways) want nothing to do with it.