Is your feature request related to a problem? Please describe.
The out-of-the-box experience is essential for Distros. As Silverblue and Kinoite use Flatpaks, these should use the system themes.
Describe the solution you'd like
Use this command (maybe another dir for other Desktops?)
sudo flatpak override --filesystem=$HOME/.themes
Describe alternatives you've considered
runing it manually
Themes for Flatpak applications are shipped as Flatpak extensions to ensure that they match the versions of libraries included in the apps. They should not be loaded from the host.
Is your feature request related to a problem? Please describe. The out-of-the-box experience is essential for Distros. As Silverblue and Kinoite use Flatpaks, these should use the system themes.
Describe the solution you'd like Use this command (maybe another dir for other Desktops?)
Describe alternatives you've considered runing it manually