It can be more efficient when combining both Alt-Tab and Alt-` - if you have several windows open in multiple different apps, it's easier to first Alt-Tab to the app you want and then Alt-` to the window you want rather than Alt-Tabbing through like 20 individual windows.

That being said, I don't really strongly prefer one system over the other; the main cost is in switching between them and using the wrong shortcut for a while (more a problem on the OS with 2 shortcuts, i.e. Linux). This would be helpful to avoid that, but so would configuring whatever Linux windows manager I'm using to only use Alt-Tab.