@matteo I'm working on making it work a bit better on GNOME based distros out of the box, but in the meantime, this should work (although untested):
flatpak override --env=QT_QUICK_CONTROLS_STYLE=org.kde.desktop --env=QT_STYLE_OVERRIDE=Breeze org.kde.audiotube

This just enables the same style that is set by Plasma.