In X11, running any flatpak app with the option --filesystem=~/.XCompose:ro allowed said apps to use my settings in addition to the default ones.
However, on Wayland (hyprland WM) this no longer works… 
Any idea why not?
PS: note that the custom key-bindings works fine on dnf installed apps such as Kitty and Firefox.
Still no solution… ¯\_(ツ)_/¯
It is quite difficult you can find a “solution”, my guess is the said applications aren’t 100% compatible with the Hyperland compositor (which handles Wyland) and/or with the Wyland protocol itself. One of the major difficulties with Wayland is many things need to be re-implemented because either some function is not included in Wayland specs or it requires a totally different approach.
The major projects like Gnome and KDE implemented a Wayland compositor but other DEs and WMs don’t have the manpower so they fall back to some third party compositor which usually is based on Wlroots from Sway. Then to maintain backwards compatibility with apps and components that work only on X11, some middle abstraction layer is needed (see for example XFCE implementation). It is complicated and messy.