The themes section on the desktop integration doc here might be of use: https://docs.flatpak.org/en/latest/desktop-integration.html
This may be useful for further elaboration: https://www.reddit.com/r/flatpak/comments/y9jmqj/the_general_flatpak_qt_and_gtk_theming_guide/
Going off of these guides my best guess would be that you don't yet have kvantum or some other theme runtime installed within flatpak
I'll also mention Stylepack exists for automating and streamlining theme installation, it's only for GTK currently however but maybe will be of use in future: https://github.com/refi64/stylepak