I reckon it'll be fine.....
if you check that the engine is clear enough of the water when it is mounted low, just cut a chunk out of the transom, give it a very severe roughing up and glass it over. A low mounted engine puts less load on the transom.
It might even be a benefit since wee Seariders like to put their bows under if you are not paying attention in a following sea.
In at the bow, out at the stern.
Might be a bit wet in reverse though.