Configurations I've Tried:
2560x1600 main, 3x 1900x1200
2560x1600 main, 3x 640x400
2560x1600 main, 3x 1280x800
Theoretically these should work fine, since they're all just scaled down 16:10s.
Interestingly, when I run a stacked configuration of 4@ 2560x1600 -- where repeater functions fine between the main and slave windows -- and add video feed windows (scaled down) with passthrough enabled on a second monitor, if you try to pass clicks through the feeds, the cursor ends up completely off target as well -- just as it did when I had scaled down slave windows.
Seems like an overall problem with scaling in D3? By that I mean scaling of mouse cursor position, not scaling of the windows themselves.
Using another repeater software like Input Director will work though, as long as all of the windows have the same aspect ratio. I could scale my VM's window from 160x100 all the way up (at 16:10) and it never lost any functionality, even in windowed/fullscreen/FSwindowed modes.
You mentioned this before, but leads me to believe it's a tweak you'll need to make in IS for D3 specifically. Hope that helps