If your linter is enforcing subjective aesthetic constraints, then I'd argue it's not really a linter but a formatter at that point, and it should be automatically fixing all that stuff for you rather than have you do that manually. Things like import order, empty lines, white space etc can all be fixed automatically in most languages I've worked with.

Linters enforcing rules that need to be broken is a pet peeve of mine, and I agree with you there. Most linters allow for using comments to explicitly exclude certain lines from being linted. This should ~never be necessary. If it is regularly necessary, then either you're programming bad (always a possibility!) or the rule has too many false positives and you should remove it.