[APINotes] Fix failing tests after a PCM logic change

This fixes tests that are going to be upstreamed in the near future.
Currently they are failing downstream in the Apple open source fork.

Failing tests
  Clang :: APINotes/retain-count-convention.m
  Clang :: APINotes/types.m
  Clang :: APINotes/versioned-multi.c
  Clang :: APINotes/versioned.m

Since 2e5af56b got merged, Clang now enables `LangOpts.APINotesModules`
when reading a precompiled module that was built with API Notes enabled.
This is correct. The logic in APINotesManager needs to be adjusted to
handle this.

rdar://123526142