With any boat you want the propeller in free flowing water. That means only just, but fully below the keel level at the transom Any deeper and you have troubles navigating shallow waters. On a Wayfarer this propeller position is easily achieved by a short tail outboard. On the other hand, a long tail may be a blessing in a heavy chop where a short tail tries to push air half the time. The question now becomes if you intend to use it in rough sea’s a lot? Or if you rather sail shallow waters with it (beaching)?
Storing it in the aft locker is no option in my opinion and here is why:
1. The weight is where you don’t want it. A better storage location is, in an engine bag, next to the CB or in front of the mast (mk1 only).
2. I never open the aft locker at sea. If it floods I am doomed. Remember that, while sailing, it is not a locker but a buoyancy tank, intended for your and your crew’s safety!
3. I consider the engine a safety device as well, hence I like to carry it at the ready at the transom. Just think for a minute about how you are going to attach the engine to the boat in a choppy sea? You wouldn’t be the first to unintentionally offer an engine to Neptune.
The special Wayfarer outboard bracket (the removable one), when mounted as intended, brings the top of the mounting board (plank?) to the exact same level as the transom. Therefore, using this sort of bracket is no reason to choose for a long tail engine IMHO.
There is more to be found on the subject if you use this forums search function and also there is a lot to be found on the Wayfarer Institute of technology (WIT) web site.