Not sure what you mean.

Under the root directory there is /home. In home there is userspace.
Userspace can reside on the same HD or partition or on a separate one,
depending on how you set it up at installation. It's exact location is
transparent to the user. There is also a root Desktop, but that belongs to
root. This is not confusing because you can only access it if you change to
root in the file manager.

I am not sure what you want in a file manager. I can "explore" every part
of the Linux file system including other Linux installations of other
drives and partitions. Nothing is forbidden to me. You just need to know
what you are doing. You need to respect Linux permissions. If you
understand them and how they work then you can explore to your heart's
content.

My chosen file manager is Dolphin, but I can do this in Nautilus or Thunar.
Linux has many file managers to choose from. In all cases you need to be
familiar with the file manager, but also the file structure
and permissions. The same thing applies in Windows with the exception of
permissions. This is something that sets Linux apart and provides a greater
measure of protection and security.

I am not sure what your complaint is. All things are possible to those who
know.