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.