The Flatpak theming issue is really annoying, yeah. There’s a rather limited pool of GTK themes to choose from in Flathub, but as long as you’re running one of those themes in your DE (assuming GNOME or other GTK-based), themes will inherit. Can’t speak to KDE as I haven’t used Plasma as primary.
Other than that, Flatpak has been great. I use it reasonably heavily on a laptop that’s slower than a Steam Deck (Ryzen 5 3500u, 8GB DDR4, 1TB Samsung 970 Evo Plus) and haven’t run into performance issues on multiple distros — EndeavourOS, Pop!_OS, LMDE, Fedora, an early version of Vanilla OS, and most recently Debian 12. On my desktop I don’t feel a performance difference between Flatpak and native.