Transom configurations, why, what, when?

[tmfd]

Alot of boats and alot of different transom setups. Some are quite low, and some have cutouts for mounting the motor, while others are straight across. On my previous boat, the po had installed plexiglass to keep water from splashing in where the transom was cutout for the motor to mount. Two pieces, one on each side of the motor. Now on my current boat the transom is lower than the gunwhales but it also is "connected" to a sort of splash gaurd that takes up alot of the stern? (rear) of the boat. Underneath is storage for the battery etc. I assume this would make the boat more seaworthy in rougher waters? As water will have a hard time getting in the boat from the stern. Ive seen bigger aluminum boats that had the transom at the same height as the rest of the boat. with no "splash gaurd" area.