RE: Engine mounting and Aircraft Datum
You know, I just looked closely at the attached pictures. The motor mount is actually constructed of wood isn't it? The beam mount is actually a couple of sticks of hardwood projecting through the firewall isn't it?
Since it's wood, if it's a very hard wood, things are a little different.
Test fit the cowling to see if it is going to look skewed with the spinner up about that 5mm. A smaller than recommended spinner might look ok to you or not. Misalignment looks worse at the top, where the spinner would stick above the cowl. A smaller diameter spinner would line up with the top of the cowling.
You can also trim hardwood motor mounts down about the thickness of the engine mounting flanges and have no problem. Don't do that unless the wood is very hard wood however.