I'm a Debian fan, and even I think it's absolutely preferable that app developers publish a Flatpak over the mildly janky mess of adding a new APT source. (It used to be simple and beautiful, just stick a new file in APT sources. Now Debian insists we add the GPG keys manually. Like cavemen.)
There is no Debian if everything was a pile of Snaps/Flatpack/Docker/etc. Debian is the packaging and process that packaging is put through. Plus their FOSS guidelines.
So sure, if it's something new and dev'y, it should isolate the dependencies mess. But when it's mature, sort out the dependencies and get it into Debian, and thus all downstream of it.
I don't want to go back to app-folders. They end up with a missmash of duplicate old or whacky lib. It's bloaty, insecure and messy. Gift wrapping the mess in containers and VM, mitigates some of security issues, but brings more bloat and other issues.
I love FOSS package management. All the dependencies, in a database, with source and build dependencies. All building so there is one copy of a lib. All updating together. It's like an OS ecosystem utopia. It doesn't get the appreciation it should.
Now Debian insists we add the GPG keys manually. Like cavemen.)
Erm. Would you rather have debian auto-trust a bunch of third party people? It's up to the user to decide whose keys they want on their system and whose packages they would accept if signed by what key.