A Linux Distro can be seen as an assembled collection of applications. For instance, the Ark linux is a bare bone Linux where you get to install everything. This allow more customisation but at the expense of more time and can also be more or less stable depending on the care that is put during the choice and installation process. A distro like Mint attempts to provide applications that the user would likely expect so it comes with a lot pre-installed apps.

Flatpak is a package manager that assist the user in installing applications. The default package manager in Linux Mint is apt-get. There's also the desktop environment, display manager ( I recommend looking into tiling window manager for keyboard lovers¹), shortcut manager, audio manager, login manager, etc. But before getting into tuning your computer, you should find a proper backup solution. There's borg, borgmatic, timeshift, etc. Note that not all backup solution are equal, some are full backup, others provide simple restoration mean. Each comes with pro/cons. There's always a risk of breaking the system and it is not always possible to recover without backups or too much work.

¹ I suggest I3 for neophyte or DWM flexipatch for more advanced users. There's qutebrowser that is a great keyboard driven browser. There's also tmux for those who just want to split their terminal and other stuff like that.