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your explanation is partially wrong...

the problem is rooted on plugins that have external system dependencies that are not aligned to what is provided or bundled in the AppImage...

AppImage's are strongly recommended to be built to a system level equivalent to the oldest Ubuntu LTS still in support, which at the time of this writing is 20.04 (focal fossa).

If some plugin uses or needs any system feature or ABI that is not backward binary compatible to that, it just fails and most surely crash the whole show.

That is the most right explanation, and again, not to general file-system organization whatsoever. It's about plugins and the jungle out there :)

sorry.