Re: How do you close last tab with the middle mouse button?
You can only close the last tab by setting that pref to false.
You can't have a different behavior for the mouse and the keyboard (there is a close Window shortcut key).
Otherwise you need open a new tab and drag that tab to position one to have the first tab as an empty tab.
If you really want to close the tab then best is to first close the tab and then close the window to prevent a History > Recently Closed Windows entry.