bpo-31845: Fix reading flags from environment (GH-4105)

bpo-31845: Fix reading flags from environment (GH-4105)

The startup refactoring means command line settings
are now applied after settings are read from the
environment.

This updates the way command line settings are applied
to account for that, ensures more settings are first read
from the environment in _PyInitializeCore, and adds a
simple test case covering the flags that are easy to check.