What reasons can you not use the lower eyelets?

In my experience with the racks that mount to the fork end eyelets- they're made to mount to the lower eyelets. The length of that strut is designed to go to the lower eyelet and the upper strut(s) mount to the fork crown and the rack is leve.

I would just use a spacer between the eyelet and the rack strut, it holds the rack strut out of the way for the fork. Moving it down and back and rotating the rack should be enough to make the holes match up and level out the rack.