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The foot control motors require less shaft length and don't hang out over the side as much. I have a tiller on my 15' which, like you, I opted for because of room on the deck but the motor does hang way out there.
I have a Minn Kota riptide 55lb. thrust with a 48" shaft. I don't use it to "troll" like one would with a kicker engine, I use it for putting and keeping the bow of the boat where I want it. Really, advice on my setup will not help you much because the 15 and 17 foot hulls differ so much as far as performance with lateral trim. In other words, how many and where the batteries are placed. Some of the Montauk owners will be better help. I just wanted to help your decision based on my experience with the long shaft of the motor hanging the controller two feet overboard and caching every wave when it gets rough lol. A foot controlled motor will be, I believe 12" shorter, therefor a lot more streamline at the bow.
I'm having a hard time picturing the motor hanging overboard. When you say "controller" do you mean the handle that controls the direction of the trolling motor? Why would it hang so far off, doesn't it just mount on to the stern?