This is actually really funny as I saw the specs have been released now for the CM3 and I had this exact same thought!!
Ultimately I'd like to redo the main board to directly take the CM3 but this could be a good lead up to it (being compatible with original boards and also anyone could have a pi3 in their project without having to unsolder the Ethernet and USB of a full size pi3..).
This would also mean an easier way to do HDMI as I would have to put the signals somewhere!
I'll have a play and see how this would work

the funny thing is that the CM ends up being a LOT thicker than the zero.. So using this may perhaps require some careful consideration not to hit anything on the other half of the case..
Other options include having VGA out on it too, such that you could use 6x thin wires to do VGA (obviously not using the original adapters, screen drivers don't need that)