A short shaft is 15"& a long is 20" to measure an engine measure from the bottom of the saddle where the engine sits on the transom & the cavitation plate just above the prop
Other all are exactly the same you may have an inch or so differance from the norm depending on the make of engine
Most engines can be run a little high on a small boat without problem I run my 40 yam ss with a17" transom & it's fine
My points about not chopping the transom on an sr4 were that lots of sr4's are not exactly in the first flush of youth and tend to be bargain basement boats & cutting the transom to fit an engine that suits the budget isn't the total no no people were saying.
Obviously it's better to get the long shaft but if you have the chance of a mint short shaft for the right kind of money then it's not the end of the world to cut the transom to suit
Just be aware the boat has a bit less freeboard at rest
When your up on the plane you won't even notice the differance