Hotkey windows do not show up in cmd+tab switcher. It's annoying if you activate the hotkey with cmd+space, press cmd+tab to go to previous window, and instinctively press cmd+tab hoping to get back to the terminal window. But that doesn't happen.
Would you mind filing a bug? The next version is focused on hotkey window improvements and this is very easy to fix. I'm away from my machine now or I'd do it myself. Thanks! ITerm2.com/bugs