[TYP] Reduce stubtest ignores

[ksunden]

PR summary

Broadly makes the type hints more reflective of runtime behavior, though does incur some type:ignore comments because of sub/superclass interactions

In particular, mypy does not approve of making parameters to methods mandatory for subclasses (it is fine with adding optional params, just not making valid superclass calls invalid).
Nor does it approve of removing even an optional param (for the same reason).

Helper _path functions which are undocumented are no longer exported in the transforms namespace.

Some additional comments added regarding corner cases of typing/explaining new ignores

PR checklist

• [N/A] "closes #0000" is in the body of the PR description to link the related issue
• [N/A] new and changed code is tested
• [N/A] Plotting related features are demonstrated in an example
• [N/A] New Features and API Changes are noted with a directive and release note
• [N/A] Documentation complies with general and docstring guidelines