I made a script to apply your custom KDE Breeze colorscheme to all your GTK3 Flatpak apps. I’m going to leave it here in case it is useful for someone.
#!/bin/bash
rm -rf ~/.var/app/*/config/gtk-3.0/
find /home/yourusernamehere/.var/app/ -maxdepth 2 -iname 'config' -type d -exec cp -R /home/yourusernamehere/.config/gtk-3.0 '{}' ';'
rm -rfv "/home/yourusernamehere/.var/app/io.github.arunsivaramanneo.GPUViewer/config/gtk-3.0"
The last line is excluding a certain app that doesn’t work well with dark themes.
Replace yourusernamehere with your username, obviously.