When I mounted my new engine on my Zodiac I had the same issue. The boat was rated for an engine with a 20" shaft so that is what i ordered. The transom was actually a little short, around 19" and the motor a little long, actually 22" so between the two there was a bit of an issue. This is really not all that uncommon. I jacked my engine up three holes and the water spray went away and performace got better. My cavitation plate is now a hair plus or minus above the bottom of the boat.
Unfortunately there is no law on actual produced lengths at least not in the US on transoms or engines so you will find variances. I've found brand 20" shaft engines with measurements anywhere from 18.5" to just over 22".
Best of luck with it !