Yeah, that's just libadwaita-QT not being up to date with GTK, sadly. It will likely get updated but there is afaik no work on adapting it at the moment, it's still very much planned.
The problem is not Flatpak itself. The problem is that Gnome by default makes non-Libadwaita apps have bold titles. The way to go is use the Gnome Tweaks tool to disable the bold text for legacy apps.