Yes, a setup like that may transfer a lot of vibrations to the fuselage sides. What I would do with a setup like that is simply remove the engine mount and sand the insides of the fuselage sides. Sand it down so that you have ~1/16"-1/8" clearance on both sides of the mount. The fuselage sides look to be thick enough that you can sand away that much material with no problems at all.

Hope this helps

Ken