Any theme can have its own theme adjuster script, which is just a script that talks to a theme. If the name of the script matches up to the name of the active theme, Reaper will serve that us the appropriate theme adjuster in the Options > Themes link. If you've made a mod of the default theme and saved it under a different name, the easiest next step would be to copy the theme adjuster script and change its name the same. Then the link will work.
The user settings for a theme adjuster script are saved in the user's reaper_themeconfig.ini file under the name of the theme.
Any theme adjuster script could be run at any time, with any theme, if run manually through the Actions window ...its just a script. Predictable results would require them to be code compatible. The Default 6 theme's WALTER contains the line
Code:
define_parameter 'defaultV6' 'defaultV6_version' 1
which means "when the script's themeCheck() functions asks if you are the defaultV6 theme, say yes". It doesn't know, or care, if that's actually true
I would say, practically, it would be a nightmare to build a theme from scratch that functioned correctly with Default 6 theme adjuster script. But if a theme were a mod of the Default 6 theme, then it starts out compatible and unless you break it or alter what different params do, it should remain so.