True form can effect supernatural transformations. The alchemist mutagen is a supernatural type and the description does state a change in shape. Could a wizard cast true form to momentarily kick an alchemists out of his mutagenic version.
True form only cancels polymorph spells and supernatural abilities that allow a creature to change shape (which mimic specific polymorph spells). It wouldn't affect an alchemist's mutagen any more than it would a barbarian's rage, nor would it cancel, say, enlarge person.