The mechanism to add custom frozen modules to the Python runtime is to set PyImport_FrozenModules (see Python/frozen.c) to some new array.  This means that the default frozen modules (from _PyImport_FrozenModules) are no longer used unless explicitly added to the custom array.  This is unlikely to be what the user wants.  It's especially problematic since it's easy to not realize this (or forget) and forgetting essential modules (like _frozen_importlib) will cause crashes.

It would probably make more sense to have PyImport_FrozenModules be an array of *additional* frozen modules, defaulting to an empty array.  Before going down that route we need to be sure that isn't going to break folks that are accommodating the existing behavior.