Btw, you can remove runtimes without first removing the apps that depend on them.
I tried first, but it just complained that Steam (and the other two Flatpaks) needed the package and it aborted the removal process.
Anyways, I uninstalled all Flatpaks as you described, removed the directories, removed the Flatpak package, did a reboot, ran a full system update and installed Flatpak and did another reboot just to be sure and just installed Steam this time.
It starts getting hilarious. Same, Friggin. Result. Installation works without any issues, update works without any issues, the popups show, the console output looks fine, and then this again at the end:
<span style="color:#323232;">GetWin32Stats: display was not open yet, good
</span><span style="color:#323232;">GetWin32Stats: display was not open yet, good
</span><span style="color:#323232;">steamwebhelper.sh[5479]: Runtime for steamwebhelper: defaulting to /home/dirk/.var/app/com.valvesoftware.Steam/.local/share/Steam/ubuntu12_64/steam-runtime-heavy
</span><span style="color:#323232;">steamwebhelper.sh[5479]: Running under Flatpak, disabling sandbox
</span><span style="color:#323232;">steamwebhelper.sh[5479]: CEF sandbox already disabled
</span><span style="color:#323232;">CAppInfoCacheReadFromDiskThread took 0 milliseconds to initialize
</span><span style="color:#323232;">src/steamUI/steamuisharedjscontroller.cpp (540) : Failed creating offscreen shared JS context
</span><span style="color:#323232;">src/steamUI/steamuisharedjscontroller.cpp (540) : Fatal assert; application exiting
</span><span style="color:#323232;">08/19 00:40:11 Init: Installing breakpad exception handler for appid(steam)/version(1690583737)/tid(5473)
</span><span style="color:#323232;">assert_20230819004011_29.dmp[5779]: Uploading dump (out-of-process)
</span><span style="color:#323232;">/tmp/dumps/assert_20230819004011_29.dmp
</span><span style="color:#323232;">dirk ~ $
</span><span style="color:#323232;">assert_20230819004011_29.dmp[5779]: Finished uploading minidump (out-of-process): success = yes
</span><span style="color:#323232;">assert_20230819004011_29.dmp[5779]: response: CrashID=bp-5698e954-748a-45d6-a5d4-7aa7a2230818
</span><span style="color:#323232;">assert_20230819004011_29.dmp[5779]: file ''/tmp/dumps/assert_20230819004011_29.dmp'', upload yes: ''CrashID=bp-5698e954-748a-45d6-a5d4-7aa7a2230818''
</span>
I’m 95% certain it has to be one of your system packages.
Since everything regarding Flatpak was removed, including all caches, configuration files and data I am pretty sure that it has to do something specificially with the Steam Flatpak because my system as a whole works properly and and all other Flatpaks I have installed also work properly …
What distro are you using anyway?
I’m on Arch. I have listed all involved application’s version numbers at the end of my original post.
Edit: Not sure if it helps, but here’s the full installation/update output: