OnlyOffice does not respect file picker portals or dark theme
There are some Flatpak apps that don't seem to respect the file picker portals or any dark theme settings. OnlyOffice appears to be one of those.
I have reported it to the maintainer on GitHub, but if there's any workarounds for this I'm all ears.

1 Reply
Partly solved: Install Breeze or Breeze-Dark in Flatpak depending on if you use light/dark theme.
flatpak install breeze
Then, go into Flatseal and set the environment variables for the app you want (in this case OnlyOffice):
GTK_THEME=Breeze-Dark