I'm really sorry but Joplin is not and will not ever be "objectively" better than Obsidian. SilverBullet is subjectively better than Obsidian though. Note taking is such a heavily opinionated matter that there's no scope for objectivity there.
lastweakness
This is just a straight up lie. Flatpaks do share libraries, both as runtimes (as seen even in the screenshot here) and through deduplication between different runtimes and runtime versions. There's usually very little bloat, if any, especially if you use Flatpaks a lot, which you probably should, given the huge number of advantages especially with proprietary apps.
Why would you want the app devs to make that? The whole problem with distro-specific packages is having to package for multiple formats and it's a painstaking process that really isn't worth any amount of time investment at all. If you're an app developer, you'd much rather just make a universal package and hope that some distro package maintainer packages your app for their distro. That's just basic common sense...
AppImage isn't a good comparison for a lot of different reasons and I think enough people have summarised that on the internet by now.