Point??
I am not from the dev team, but this sounds very odd. Iām fairly certain that there is not that much difference between EOS and Arch considering where Wayland socket is placed at, because after all EOS is Arch made easy.
What is this about?
?? 
Element Desktop flatpakā¦
Does not run on Wayland and is using XWayland instead?
EndeavourOS does not even ship with flatpak used, nor do we change socket for Wayland (what ever this even would be for)
I can see if I can reproduce the issue if it is this.
@Twig should tell a story or make a video?
https://youtu.be/qumB54aI1bU?si=ujAW14cxJrkba0Nd this is very confusing to watch at this hour of the night 
I will have a look tomorrow
Oops, forgot to answer to you. 
As @joekamprad told, problem was really odd. OP has issues with Wayland socket that was placed in wrong place and it didnāt work on package XYZā¦ andā¦ andā¦ I really didnāt get the point of this post or his bug report.
Damn confusing. 
It didnāt make any sense to me either. No flatpak here.
Element desktop is electron, is like all chromium based must need a electron-flags.conf sometimes electronXX-flags.conf and set on ozon and wayland is not a automatic proces is mostly with all electron based
I got the wayland backend working by entering the āELECTRON_OZONE_PLATFORM_HINT=autoā enviroment variable but as you can see the people over at elementās flatpak told me this was something related to my distro
flatpak idkā¦ dont have that also 
got several electron configs lol
Create:
~/.config/environment.d/30-electron-ozone-wayland.conf
add
ELECTRON_OZONE_PLATFORM_HINT=auto
Save and restart the computer.
check with
echo ELECTRON_OZONE_PLATFORM_HINT