It's actually relatively simple. With the new scripted triggers introduced in the latest patch, all one needs to do is to go into the specific mod you want to make compatible, use a program like Notepad++ that allows you to find all instances of:

is_country_type = default

and replace all instances with:

is_zofe_compatible = yes

Tada!

As a gesture of goodwill, and to prove this fully armed scripted trigger to be operational, I have nuked most events in the vanilla game the same way, and making overrides or compatibility patches have never been easier. It won't fix 100% of all problems, but it will probably fix 99% of all problems. If you want to fine tune it and search for every instance and judge for yourself which to use where, then feel free.

Those who make compatibility patch will only have to update whenever the other mod updates, since this scripted trigger will stay the same and will never have to worry about ZoFE updates.

Thanks all!