What is the difference in /home locations between nautilus and the command-line?

I think Nautilus just changes the actual path to visually show 'Home' instead. The path is not different in Nautilus, it just shows it like that in the GUI.

Press Ctrl+L in nautilus to view the actual path.

Nautilus use the word "Home" to identify your /home/ directory.

When it shows the path in the breadcrumb, the first "home" is the actual /home dir, and the second one ("Home") represents your /home/ directory.

This substitution makes sense is some cases - I think it's easier for the user to identify the home folder by the name "Home", instead of the username. But it can be confusing in situations like this, though.