Personally I have enough extra weight and don't need the battery weight in the boat. There is a certain amount of scrambling this old fat guy does in the boat during sailing.  Extra stuff is not welcome. And I don't want anything in the way back at the transom to tangle with the running rigging of the boom.  Lines that go to cleats at the stern.  After all auxillary power is what the oars are for when the wind is light. 

My son and I set up our Passagemaker Dinghy with a modified trolling motor as an option, but we intended to leave the sailing rig ashore when using it, i.e., she's either motor + oars or sailing + oars, but not all three at one time.  We had to cut down the shaft (the vertical strut) to make it work and rewire it with heavier cable so we could have the battery amidships strapped to the daggerboard trunk.  We'd have had to move/widen the motor cutout to have both the rudder and motor mounted simultaneously, and we didn't think it was worth it.  We also thought that switching out the rudder for the motor to go from sailing to motoring was too much bother and too much clutter in the boat.

The PMD is a somewhat beamier boat vs. JSII, with a much broader transom.  I suspect things would seem a little "crowded" back there with a motor mounted next to the rudder.

Mind you, I don't think that having the motor offset from the centerline would, in itself, be a big problem at the speeds we're talking about.  However, I think that having it hung there on the transom all of the time would create some serious opportunity for getting the sheet hung up in it, which could be disastrous.  Rope just wants to have fun, you know; best not to give it too much wiggle room for getting up rope tricks.  <;-)

.....Michael