Peter,
I would be surprised if that lower outboard gap should disappear when car is on it's wheels... as you will get bending on the frame, that should not give a 3 cm outboard movement at all. I have never seen such thing, in fact, I would be very concerned driving such car. In addition you did reinforce the tubes to minimize bending.
On the other hand if that theory would be correct, don't paint the car as long it is not on wheels...otherwise paint will fall off when panels will be stressed / deformed by 3cm ;-)