This was reported in MC-60590. The issue was reported to be resolved on 11Jan2016, as working as intended. But as of testing on v1.9.4, villages and ocean monuments are still not being generated on custom biome sized maps even though the option to generate structures is set to true.

So I would like to reopen the issue. The big issue is Ocean Monuments, as there is not a way to get those unique resources without cheating on a survival custom biome sized map.