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I think you should have added the "MX Linux with Steam flatpak part" in the headline, as it sounds as if the issue is specfic to that, unless if your friend has a different system.
If the mods are not showing up in the Mods tab of the launcher, then they might still be downloaded, but into the wrong location. That's at least the case on Windows for me where they end up in Steam\userdata\170536921\ugc\referenced..
PS:
Either way, it's usually better to ask rather technical questions in the general forum.
I don't get the impression that a lot of people look here.