Add PyPI registry correctly to pool depending on other sources (#3406)

In the event where we defined sources that were set as
secondary = True, we would end up with PyPI being after this source
when it should have acted as default in that case.

The main issue stems from the fact that it's not because you have
sources configured that PyPI should not be a default. Instead, PyPI
should be default if there are no sources with secondary = False and
not default if there are sources with secondary = True.