I took a quick look at my Gyro SE this morning and I'm assuming you plan on using a second Michell armboard in the spot where the motor is located. Moving the motor outside the "ear" shouldn't be a problem however there is another issue you might want to consider if you plan on doing this. First yes the holes need to be precisely positioned, but the biggest problem I see is that on the underneath of the "ear" where the armboard is mounted from the factory the casting is much thicker and allows the holes for the armboard to be threaded. The "ear for the motor is not like this and is only about 3/16" thick so even if you tapped them to accept the mounting screws it wont be very secure (in my opinion) and could easily be stripped by overtightening! I would thing you would want to bond some appropriate nuts on the underneath of the casting to accept the mounting screws. Personally that's the biggest problem I see and would be a deal killer for me, also the reduced resale value.
Wes
Wes