Its quite acceptable to vary the FC mount location. The gyros don't care where the FC is mounted at all. The accels care, but they are only used in self leveling modes like Attitude, Rattitude, and all GPS flight modes. And of course if you use a camera gimbal that gets signal from the FC. Basically if you are flying in a non-leveling mode like Rate (and don't have an FC controlled camera gimbal) it just doesn't matter at all.
I believe that the only time it matters is when you do a fast rotation about an axis that the FC is not centered on so that you get some centrifugal force. If the FC is off center horizontally, it matters when you do yaw pirouettes. If the FC is off center vertically it matters when you do flips in any direction.
Another thing along the same line that seems to matter is the GPS offset when you do pirouettes in GPS flight modes.