bpo-28411: Isolate PyInterpreterState.modules (#3575)

A bunch of code currently uses PyInterpreterState.modules directly instead of PyImport_GetModuleDict(). This complicates efforts to make changes relative to sys.modules. This patch switches to using PyImport_GetModuleDict() uniformly. Also, a number of related uses of sys.modules are updated for uniformity for the same reason.

Note that this code was already reviewed and merged as part of #1638. I reverted that and am now splitting it up into more focused parts.