[PF] How does metamagic casting time interact with non-standard casting classes?

[AnonymousPepper]

Pathfinder metamagic lists a set of distinct categories, but it was made before any of the advanced classes and such came out, so many of the later classes are in a weird place. Arcanists are both prepared and spontaneous at the same time, Inquisitors are both divine and spontaneous, etc. Is there clarification on this somewhere?

http://www.d20pfsrd.com/feats/metamagic-feats