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.
I agree that launching flatpaks outside of a GUI is stupidly verbose. I certainly would never use flatpak for cli tools, and I think that is a problem for it. I would love to see more tools bundled up that way, but flatpak is far from the solution. And Docker has the same or bigger problems.