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On the contrary, the first time I manually installed Arch following this beautiful guide it massively helped my understanding of how an OS works. Specifically step 3.2 when you chroot into the new system.
Well, the NixOS part of it is on GitHub: https://github.com/NixOS/nixpkgs (that's where the Nix Package Manager gets its configurations), unless I override them.
2) Well friend, this is where you can have the best of both of worlds. You can just open the file explorer via the CLI. Typically you'll have the xdg-open command that opens the directory in your default file browser. I have that aliased to xdgo. So you can navigate quickly to where you need to be, and then open it visually with xdgo . . There's also other really convenient navigation tools like z (https://github.com/rupa/z) that I can't imagine going without anymore.