In an ideal world the gearbox and diff flanges would be perfectly in line but unless you're using a live axle which is going to give a large variation in axle/gearbox alignment then its not going to be an issue. As long as there is sufficient fore/aft movement (which will be minimal) of the propshaft I don't see a 25mm difference as a problem. My camper van is based on an Iveco 4.1 Tonne van and the gearbox to axle vertical distance at rest is about four inches (100mm) and this can vary by probably a similar distance, that's why we use flexible couplings.
D.
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