I can’t read of change the keys inside org.gnome.desktop folder. The values displayed by Flatpak application are different from displayed by dconf command and editing a key in Dconf-editor doesn’t change this key in dconf.
The other keys can be edited.
You can’t (normally) change dconf settings from within a Flatpak, as the dconf database is read-only inside the Flatpak sandbox. Also, as you obviously try to set the Theme for Flatpak applications to your globally set theme, read the following:
https://docs.flatpak.org/en/latest/desktop-integration.html
tl;dr: you can’t.
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