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.

Python/bltinmodule.c

@@ -2685,7 +2685,7 @@ _PyBuiltin_Init(void)
         PyType_Ready(&PyZip_Type) < 0)
         return NULL;
 
-    mod = PyModule_Create(&builtinsmodule);
+    mod = _PyModule_CreateInitialized(&builtinsmodule, PYTHON_API_VERSION);
     if (mod == NULL)
         return NULL;
     dict = PyModule_GetDict(mod);