Delay calling linter factories until modify_defaults

[MichaelChirico]

Closes #2909

This still has some kinks to iron out, but feels more promising than the earlier approach.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.24%. Comparing base (d6afa52) to head (cb6e6ee).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2912      +/-   ##
==========================================
- Coverage   99.24%   99.24%   -0.01%     
==========================================
  Files         128      128              
  Lines        7267     7262       -5     
==========================================
- Hits         7212     7207       -5     
  Misses         55       55              

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[MichaelChirico]

@Bisaloo any thoughts on this proposed fix? feels dirty but I'm not sure how else to approach it.