When I set iTerm2's hotkey mode on Mavericks, opening the hotkey window also brings any open non-hotkey terminal windows to the front. Is it possible to have iTerm bring focus only to the hotkey window rather than bringing all its windows into focus? I've considered running two iTerm processes, but since they source from the same preferences file, I can't turn the hotkey off for one and on for the other.
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.
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.