iTerm2 hotkey window activates non-hotkey windows

Solution 1:

This issue is fixed on iTerm2 +3.1 which is a nightly build, from the author's issue tracker https://gitlab.com/gnachman/iterm2/issues/644:

This is fixed as part of the big hotkey window re-do in 3.1, currently available in the nightly build.

Solution 2:

I've been curious about this as well and this is a really temporary solution that I'm not happy with--but it's something.

By simply minimizing your main terminal window (instead of leaving an active iTerm window in whatever desktop space it's in--which I'd much rather do) your hotkey window will drop down the visor in your current window without conflicting with the main terminal window.

NOTE: this will only work in desktop spaces and not in full-screen ones. If you attempt this in a full-screen space it will open your hotkey window in the nearest desktop space.