To run a flatpak app from dmenu, you can create a symlink for the app in /usr/bin.
You can find the flatpak apps binary link in /var/lib/flatpak/exports/bin/ on ubuntu.
E.g. to run Rocket Chat (installed from flatpak via software center), you can do something like this:
sudo ln -s /var/lib/flatpak/exports/bin/chat.rocket.RocketChat /usr/bin/rocket-chat
This way you will be able to find it in the dmenu.
Resources:

Maybe this could also work with dmenu or similiar.
With
rofiI was able to list all installed flatpak applications. Just add this to your i3 configuration file before your dmenu command: