Thanks, I've just responded to your PM :).
Putting this thread a bit back on the topic of multiple profiles specifically, the Flatpak also stores its data elsewhere and should be enable you to have at least the one AppImage version and Flatpak instance side by side. Unfortunately I'm unsure if the same Flatpak can be installed multiple times though.
What you might find interesting is how the snap actually relocates those folders. The Flatpak uses a mount namespace to trick Joplin into writing to the "wrong" folder (inside the Flatpak namespace). The snap doesn't. Joplin doesn't respect the XDG Desktop specs for placing its data; the only thing that needs to be changed is $HOME itself.
So E.G, you could try:
HOME=$HOME/joplin-work-profile ./Joplin.AppImage
And this might get you reasonable results. It won't unfortunately get two versions open at the same time by itself, but might be slightly more reliable than the --profile flag.
And that's essentially what this does, which is a feature of the AppImage format itself.
https://docs.appimage.org/user-guide/portable-mode.html
Unfortunately, this all misses fixing the actual restart problem, since there'd likely still be only one app running at the same time. (And I unfortunately never figured out how the snap actually avoids that).
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