My 2007 Mark II's blower opening does not line up with the opening in the stove. 1/2" vertical mismatch. Reason: the blower housing hits the 1/4" plate steel rim at the stove bottom before the blower flange fully seats into the three sided slot. Not a killer issue.
A 2-3" long cardboard plenum was jury rigged to align the two openings and found (hand test) that the CFM out the two frt openings is slightly greater. The stove/fan assembly is a lot quieter, too. Maybe a sheet metal duct or flex pipe connecting the two openings would work...or start grinding the rear edge of the stove away (not gonna happen).
Cooper, I'm not the guy to ask about long term vibe issues on Harmons but I did make a cardboard tube between the stove inlet and blower inlet and any vibe coupling that there was between the blower and stove went way down. So all that kind of suggests some sort of metal tube or exhaust pipe flex hose could be made to separate the two.
I guess one thing that is not good is leaving the blower in place with it OFF and then really cranking the stove. The heat can't be great for the blower windings, etc.
Just my opinions that are sometimes less knowledgable that others of more expertise.
You could try making a cork gasket and put it between the blower and stove to see if that will cut down on some vibration. Also try loosening or tightening the blower bolts to alter or delete the sound.
I just move it around till the noise stops. Have not made any attempts at gaskets. It is the metal on metal vibration that makes noise. Isolate the vibration noise goes away. Remote axial fan, aluminum flex hose, adapter with gasket, staged thermostatic fan control.... Now that is a plan