I am not sure because every boat is different, so upload some pictures so we have a better understanding. From what I can understand you will probaly be ok just allow some room for operating in rough water.
Having the head of the trolling motor be too high might be a pain to fish around and stow. You might be able to cut the shaft and reconnect depending on the motor you have. Look for a post by Ranchero in the mods. He documented the process as described.
You can get away with whatever you are comfortable with. A longer shaft will get ing the way some both when it is deployed and when it is stowed. I have a 52" shaft on my 16' mod V and it can be a pain. But you can't complain when a 54# 24V trolling motor cost you 100$. I learned to live with it. Under different circumstances I would have bought a shorter shaft model if the price were even close to even.