Yep. The main way I notice that an app is using FlatPak is it becomes impossible for me to type Japanese in it because the person distributing it hasn't done the complicated stuff you have to do to make IME work with FlatPak.
I really hope Wayland helps here. It has an IME input API, so if that's sufficient, maybe it can displace out-of-band input buses on the application-side.
