the one in user/Maya/scripts is there for all installations of Maya ( all versions)
the one(s) in user/Maya/2020/scripts or user/Maya/2021/scripts/ or user/Maya/2022/scripts/ are per installation version ( not all scripts work in all versions of Maya ,, as changes to base code happens)
the one in projects/[ project name]/ will only get sourced during the setting of the project For that project. So it's a great way to globally share scripts with everyone on a project.
I'm not sure where the pain lives.. Just drop it in user/maya/scripts/ that will work 99% of the time.
Unless it's for a specific version of Maya.. then user/maya/[version#]/scripts/
I wouldn't recommend messing with the ones in program files / autodesk / Maya / version etc. ( there is no need to )
hth
-=s