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If I have a root account that can be logged in to it always had a different password. Is there something I'm missing here?
No, that's a good choice. It reminds you to be cautious when logging in.
Some people have trouble remembering 2 and set both to the same. It's probably better to use sudo instead.
sudo password, user in the wheel group
Thats why using sudo or polkit is not that nice.
Making Linux work with a non wheel user is already nontrivial