Can Break Enchantment end the effect of an Alchemist's mutagen or a Master Chymist's mutagenic form ability?
No. These class abilities are neither an enchantment (school of spell), transmutation (school of spell) or curses. In addition, they are supernatural abilities which mean they cannot be dispelled. Extracts carry a clause that their effects can be dispelled (and list which school of magic they belong to), while mutagens/mutagenic form do not carry the same language. The only way to stop them is an anti-magic field.