ThemeChanger VS Gradience

I think flatpak tries to follow whatever theme you set in your DE. You could be lucky with this tool https://github.com/ALEX11BR/ThemeChanger

If your main problem with Adwaita are the colors, you can easily customize them, and there are even great GUI tools for this[1]

My issue with Breeze aren't the default colors, but rather the theme itself

[1]: https://github.com/GradienceTeam/Gradience

I really like GTK4 / Adwaita and dislike the look and feel of QT, but I guess that's just personal preference.

You can change the colors of Adwaita using https://github.com/GradienceTeam/Gradience it even has a mode to extract colors from your background like current android versions

Application Theme : adw-gtk-3 with Gradience

This might be an alternative for now - https://github.com/GradienceTeam/Gradience

if the app is using libadwaita you cannot modify the css, you can use gradience to set custom colours though, but it is not the same as modifying the css

For everything else I use the only tool available for properly configuring GNOME: dconf-editor. At this transitional time, managing themes is a challenge, but I like Gradience.

You could also use themix or Gradience

Try https://github.com/GradienceTeam/Gradience/ .

You've tried Nord from Gradience ?