Tiny MCE default font size overrides Theme Settings

I guess you are referring to the user being able to set the font size as inline CSS on spans?

Why can’t there be a setting in the plugin that stops it from overriding default font sizing?

There is: remove the “Font Size” button from the editor toolbar.

Why is the standard advice to go make changes to PHP

Not sure what are you referring to but it doesn’t sound like a good advice… Definitely not the “standard” advice 🙂

I agree, letting the user set font sizes as inline CSS can be pretty hard to change/fix later, but… As far as I see the alternative is to add standard classes that all themes support. Not sure that’s realistic though.