I am currently using Linux Mint (after a long stint of using MX Linux) after learning it handles Nvidia graphics cards flawlessly, which I am grateful for. Whatever grief I have given Ubuntu in the past, I take it back because when they make something work, it is solid.
Anyways, like most distros these days, Flatpaks show up alongside native packages in the package manager / app store. I used to have a bias towards getting the natively packed version, but these days, I am choosing Flatpaks, precisely because I know they will be the latest version.
This includes Blender, Cura, Prusaslicer, and just now QBittorrent. I know this is probably dumb, but I choose the version based on which has the nicer icon.
That’s not all that different than a traditional package manager. You’re downloading the dependencies either way. With Flatpak, they’re bundled in. With a traditional package manager, it just fetches all the dependencies and shows you that they’re being installed one-by-one. Either way, it’s one command to install.
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You’re correct that Flatpak solves that problem, and there’s some value there. But you can also solve the problem by just having two versions of Python or two version of libjpeg or whatever installed, and then you as the user/admin manages ensuring that each program uses its correct dependency. That’s certainly more difficult, but I’ve just not found it to be problem that is both frequent enough and difficult enough to solve that I would personally value the tradeoff in overall complexity of adding Flatpak to the way I manage and use my systems.