How to change colors and theme settings in 'Windows Store app' version of Arduino IDE?
I think rrz0's answer skipped the part of the question:
"For the Windows Store app version of the IDE the theme files are stored in protected app storage space."

The only way is to take control of the windows app folder but I believe this is risky and M$ suggests that this can brick your pc (take that with a grain of salt).

There is an offline windows installer and zip link on the downloads page which I used to replace the windows store version. I see no advantage to the store version.