A couple of things to consider when designing the transom locker:
1. Deck drainage: Ensure you can get any water on the deck to the elephants' trunks. You could run round ducts through the locker.
2. Outboard tilt: The transom is cut down on a SR5.4, so make sure you are able to tilt the outboard up without it or its cables, hoses, etc fouling on the top of the locker.
Good luck