The gearbox plays no role in the remapping and most powerful cars nowadays come with an auto box, so nothing to worry about that. But, you will not gain anything serious by remapping a NA engine. If you rebuild it you could potentially gain something but then the engine will not suit the requirements of a family car and it will have cost you a fortune. You have much bigger gains with turbo engines but there is always a trade off to pay at some point such as shortening the life of the clutch, gearbox, etc. The small gains you may get from remapping your engine, probably will not cause any troubles to the auto box.