More pictures of the gunwhale and cushion would help but I hope this is clear enough and maybe it would work for you.

I would put a 1/4" aluminum backing plate under the gunwhale then cut a 1/4" plate to exactly match the Scotty base plate. Move the Scotty base and aluminum plate inboard until you can thru bolt the outer 2 mounting points and the inner 2 points are inside of the gunwhale. Mark the location and bolt both aluminum plates together thru the gunwhale with the bolts in a location that allows for the Scotty base to be mounted over the top. Thru bolt the outer 2 mounting points and it looks like you should be able to bolt the inner 2 points thru the aluminum plate and clear the cushion. You could mock everything up with wood and have the plates cut by a machine shop.

Or you could just add the backing plates under the gimbal mounts and save the extra holes in your boat.