this might be asked many times already as flatpaks dont have access to system files to respect system global theme so could it be possible to install default breeze dark/light themes as user and install those as global to get all apps respecting system theme.
i saw somewhere post where stated downloading global themes and using install option to usr folder to get so called unified global theme
I am on Fedora Workstation, not Kinoite, but an interesting thing I have noticed is that as I installed a theme for legacy-gtk apps (adw-gtk3-theme) as RPM from the repos, then a flatpak update also installed the same theme as Flatpak (probably as some kind of “dependency” of org.gnome.Platform).
The installation of the Flatpak theme happened not right after installing the RPM theme, but rather after activitating it (via GNOME Tweaks).