Congratulations on your new machine and on running Linux as your daily driver.

Best practice is to follow the install advice of the devs. Some devs only release through terminal/downloads, others prefer to release an app image for wider compatibility and OS integration, others have an official Flatpak. Some Flatpaks and Snaps have reduced functionality, others do not.

Distro repos can be slower to get updates, but it depends on the devs preferred release channels.

Sometimes there's no choice if the app isn't available for your distro but to either compile it yourself, use it in a VM running the compatible distro, or use a third-party Snap or Flatpak.

If you have to use an unofficial third-party Flatpak, then Flatseal is your friend. It helps you manage Flatpak permissions.

If you really want to dig in to a Snap or Flatpak but you can't read code, then copy the contents of the code into GPT or Claude etc and ask it to search it for malicious code from the files.

Updates will happen differently depending on how you installed the software. Traditional repository packages will update when you run system updates (like sudo dnf upgrade), but Flatpaks and Snaps have their own independent update systems.

Flatpaks update through the "flatpak update" command, while Snaps are designed to auto-update by default. Many Linux users create simple scripts that run all update commands together, or use software centers like GNOME Software or KDE Discover which can handle updating all package types through a single interface.