> Q: How to solve the problem?

Making sure that the "total reference count" is zero after Py_Finalize() is a long term project which requires to solve many subproblems:

* Convert static types to heap types: bpo-40077
* Somehow related, convert extension modules to multiphase initialization (PEP 489): this issue
* Identify remaining global variables and either clear them explicitly, or move them to a structure which is cleared at exit

To convert extension modules to multiphase init, one practical problem is that the PEP 573 doesn't cover slots and a few other corner cases. The PEP 573 should be extended:
https://mail.python.org/archives/list/capi-sig@python.org/thread/6CGIIZVMJRYHWZDJLNWCLPSYYAVRRVCC/

There are likely a bunch of other misc corner cases which should be fixed as well.