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I am not sure whether this is still an issue. When you run the AppImage e.g., from /opt as root, then it could/should install the desktop integration system-wide for all users.
But I am focusing on appimaged instead these days.
I am not sure whether my original request was really what we need, it seems from AppImageCommunity/appimaged#30 that per-user desktop integration is also sufficient for those applications that are available system-wide. Hence, closing.
[desktopintegration] When installed systemwide, then do not ask user
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