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 you are asking about permissions so yes. I often limit access filesystem paths, dbus proxy, devices and network.
That is a good deal. I was briefly under the impression that those were not accessible, but that would be totally against the principles of everything Linux is about. So permissions set by the developer are just their biased defaults, nothing permanent.