I tried
sudo flatpak override --filesystem=$HOME/.themes
sudo flatpak override --filesystem=$HOME/.icons
and it did not work. I'm not sure if choosing a specific theme would work or not.
I'm using Breeze, colors set to match my wallpaper, and I don't know which Breez theme to specify in
sudo flatpak override --env=GTK_THEME=my-theme
sudo flatpak override --env=ICON_THEME=my-icon-theme