I guess it depends if they measure the transom from the bottom of the boat to the top of the transom or the top of the tunnel to the top of the transom. I measure from the bottom of the boat to the top of the transom and it's around 23". From the top of the tunnel it would be around 20.5" and you can see my motor is mounted 2-3" above the transom. It could depend on the jackplate you get on how much rise it will give you. But even with a short shaft engine, you might need 5-6" of rise above the 21" transom to get the motor up behind the tunnel. I'm pretty sure the skeg will still stick down below the bottom of the boat either way. This looks like a situation where you need to talk to a lot of people to figure out what will work best. If you get the 21" transom and then need to run the jackplate all the way up, the jackplate is then worthless is you wanted it for flexibility of motor height. I've never dealt with a prop tunnel but I'll search around to see if there is any good information or pictures to help. And yes, it's not easy finding a short shaft motor so that might be the hardest part of your plan.
edit: It's tough to find good information and pictures on prop tunnel setups. I think with a tiller, it will leave your arm pretty high whether you have a 21" transom or 27" since the motor will be up to get the prop in the tunnel area. Here are a couple of pictures of different boats to show how high it might need to be. I can't tell if these are 20" (long) shaft or 25" (extra long) shaft motors