I raised mine and am glad I did. I also raised the floor and put in larger scuppers. If you put two or more guys in the back and there is a baitwell, and you are anchored in any sort of chop, those extra inches keep water from coming in. With the floor at the right height, the water that does come in drains quickly.
My 150 Yam carb is on the transom. Planes real fast, little if any bow rise and great attitude under way. I have never ridden a bracketed one and have not heard whether putting the weight back affects the ride negatively. Good luck.