The official AppImage wouldn't have any problems using the external editor functionality, so if it's important to you then it could make sense to use it. You'd only realistically be losing automatic updates. You could either export your current notes as a .JEX and import them into it, use the sync functionality built into Joplin, or open the profile directories and copy them over (whilst they're both shut down ofc). The AppImage is also the only Linux choice that gets official support.
It's unrealistic for me to claim the packages make sense for everybody, they're fine for a lot of people but the external editor functionality is a weak point and it's unlikely to improve in the future. Though if you do appreciate the sandboxing and automatic updates these packages bring, the Flatpak gives much more control over the external editor than the Snap can.
Ultimately it's your choice based on your own circumstances.