In general, defaults set via the Macro Panel stick around. But, they are not as future-proof as options that have progressed to get their own UI. This is how new options are often introduced: As a hidden user default first so that people can try and if it proofs to be generally useful, it should get a UI sooner or later. The same applies to the background layer color.
That would be the following:
It’s set per font, not globally for the app. That might be why you are not seeing its effects on new font files.