[Pygments] Check for missing stubs outside omitted subpackages

[brianschubert]

These stubs are basically complete, but ignore_missing_stubs = true was set back in #9779 due to there being a few deliberately omitted modules. This adds allowlist entries for those modules instead, and fixes a few inconsistencies that have accumulated.

[github-actions]

Diff from mypy_primer, showing the effect of this PR on open source code:

sphinx (https://github.com/sphinx-doc/sphinx)
+ sphinx/highlighting.py:39: error: Unused "type: ignore" comment  [unused-ignore]
+ sphinx/highlighting.py:39:5: error: Cannot assign to a method  [method-assign]
+ sphinx/highlighting.py:39:5: note: Error code "method-assign" not covered by "type: ignore" comment
+ sphinx/highlighting.py:39:35: error: Incompatible types in assignment (expression has type "classmethod[Any, [Any], Any]", variable has type "Callable[[Any], GenericAlias]")  [assignment]
+ sphinx/highlighting.py:39:35: note: Error code "assignment" not covered by "type: ignore" comment

[brianschubert]

sphinx hit is a true positive. The affected line is already covered by a # type: ignore comment, but the error code changed now that Formatter.__class_getitem__ exists in the stubs.

https://github.com/sphinx-doc/sphinx/blob/cc7c6f435ad37bb12264f8118c8461b230e6830c/sphinx/highlighting.py#L39.