It's not a fire vulnerability. It's just that chemical change stops the regen.

Just because burning cut troll flesh makes it not regen doesn't mean that it will penetrate. They're not highly flammable like Twilight/Luminosity vampires. If I was designing Muggle anti-troll weaponry, I'd be going for something to penetrate into the body and then spread incendiary material. Not a flamethrower. (Although first physically injuring trolls and then dousing them with napalm might work, sort of.

Incendio in the troll's eye would just burn out the eye.

Mana cost in HPMOR seems to affect cooldown more than castability of spells, and transfiguration seems to have no cooldown but (for Harry, Q and other powerful wizards are much faster) is time-consuming.

Harry should be able to near-instantaneously slice-and-dice any transfigurable object by using very thin cutting boundaries, and even cause explosive separation by using compressed inert gas, or even a friction-sensitive explosive (most explosives form fairly nonhazardous materials) Even if the acid failed to prevent the regen, he could have dismembered the troll temporarily and bought time to try something else or to burn it.

ETA: Also, Harry is now able to predict what forms of transfiguration are dangerous, and mild transfiguration sickness is not