I've been in favor moving that shaft back for a while now, especially to allow for that torpedo bay and that corridor, and definitely in the case of the E-A.
As for that "deflection crystal", I think the biggest argument in favor of not having to connect the intermix shaft to it is the Reliant. After all, it's got two of those puppies, dorsal and ventral, and no real room for the same sort of intermix shaft.
It might be best to just chalk up the Enterprise's engine setup as something of an experiment (goes right along with the idea that the refit is a prototype).
Yes, I'm starting to ramble.
Sure, move it back, screw the deflection crystal.