Fixes flag default handling for boolean options

[john0isaac]

Ensures boolean flag options correctly determine their default values when not explicitly set.
Adds tests to validate proper behavior for various flag configurations, improving reliability.

Fixes #2897

[john0isaac]

Although it's the same issue this won't fix #2894 as it's talking about type=str, the fix would be to revert back the changed lines completely but it will break the introduced behaviour in #2829

Maybe we can revert the lines back but with flag_value = not bool(self.default) transforming it to a boolean first before negating it? this will fix both issues but it will still change the behaviour introduced in #2829 but it will no longer raise ValueError for numpy.ndarray or astropy.units.Quantity as they will be casted as a boolean.

Please let me know what you prefer.

[davidism]

Thanks for working on this. A contributor at the PyCon sprint ended up looking into this more and fixing it in a way we think is a little more correct in some cases, see #2930.