I use a dual screen setup. I have set up keyboard shortcuts for switching desktops on all screens, i.e. when pressing Alt-1 I switch all screens to desktop 0. In the advanced focus settings I have checked "Refocus last window on desktop switch".
When I have two gui applications open on one desktop, one application per screen, and I switch to this desktop using the above shortcut, e will always focus the window on my primary screen even if the last active window had been the one on the secondary screen.