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 like them for convenience, I don’t like them for customability, possibly just because I don’t know enough about them.
That is a good point I have not encountered too often. I don’t tend to customize the programs I use. I tend to just learn the defaults for that program.
Anyways, people keep recommending FlatSeal, which is a graphical way to customize Flatpak permissions, so that may be helpful to you.