Handle F401 exclusions more granularly

[Repiteo]

Was originally going to be a separate stylistic dive, but this discrepancy caught my eye so I wanted to handle it now. This removes the per-file exclusions of F401, instead handling them on a per-include basis. Also removed the exclusion from test files, as those are already explicitly setup to NOT get checked by Ruff

Contributor Checklist:

• I have created a new test or updated the unit tests to cover the new/changed functionality.
• I have updated CHANGES.txt and RELEASE.txt (and read the README.rst).
• I have updated the appropriate documentation

[mwichmann]

For Util, the correct answer is probably to add things that are "module global" to __all__. I didn't do that when I split the one giant file into a package three years ago (d83d7cf)