Every boat is built differently. If you have a 15" "shaft" motor, then theoretically you'd need a 15" transom....BUT problem is, every manufacturer is a little different. Tohatsu's 15" might be 15.750" from the clamp to the AV plate. Yamaha might be 14.875". Etec might be 15" even. All examples. They're "supposed" to be the same but there are differences.
Then boats....war Eagle uses a 16" transom, which works with most 15" motors. Tracker might use a 15.5" transom. Same with the motor deal, they're all different-just slightly.
So what you're seeing is a rigger who installed the motor in the best safe position. You might not like it. But there was at some point someone (or some people) who griped about water running up the leg and into the motor well, or griped about being slow. So they figured, hey lets raise the motor a little and solve those problems.
This type stuff is exactly why working for the public sucks. Screwed if you do it one way, screwed if you do it another. Can't please everyone. And honestly I'm about to give up trying.