
AwesomenessDog |

This flask of volatile chemicals contains traces of graveyard dirt and a few drops of blood from a righteous creature. You can throw a bone burn flask as a splash weapon with a range increment of 10 feet. Against non-undead creatures, a bone burn flask functions as a normal flask of acid. Against undead creatures, the bone burn flask deals double damage. On the round following a direct hit, a skeletal undead damaged by a bone burn flask takes 1d6 additional points of damage (Reflex DC 15 negates).
This might be a GM decides, but I'd assume by the wording "[it] deals double damage" to be following the same rules as Mighty Charge/a lance charge where everything except bonus dice are doubled. Even with a +10 Int alchemist running Imp Vital Strike, it's not that busted anyway.

Azothath |
So Bone Burn acts as Acid, but against undead it does double damage. Would this double both the acid damage and the Alchemists Int bonus to damage with alchemical weapons as well?
Alch Wpn: Bone Burn $25. it is stylized as [acid].
Alchemists - Throw Anything (Ex): All alchemists gain the Throw Anything feat as a bonus feat at 1st level. An alchemist adds his Intelligence modifier to damage done with splash weapons, including the splash damage if any. This bonus damage is already included in the bomb class feature.
and the Empower Spell FAQ {there might be a more direct FAQ just not finding it at the moment}
so yes. If you are playing an Archetype make sure it did not trade away the Feat.