Ceriani yokes are at a different angle to the steering head on the frame.
If you look from the side you see the forks slope differently to the angle of the steering head.
Marzocchis are parallel to the steering head.
So if you use a Marzocchi lower and a Ceriani top yoke then unless they have been modified somehow they in theory shouldn't match up.
On my bike with Ceriani forks I had the steering stem removed from the bottom yoke, the holes in the bottom and top yokes welded in and re-drilled to be parallel to the steering head angle.
A lot of work.
I would think either your top or bottom yoke has been modified, otherwise as you slide the fork stanchion up through the bottom yoke it wouldn't match up with the hole in the top yoke.
You can see how the top nut is offset in the yoke as the hole had to be drilled to allow steering stem an steering head to be parallel.