Matt & Michelle,
Generally agree with your observations (terrible installer, etc.). However, when you say Beta must build and test "all options presented to potential customers" to receive a Kubota warranty, I would be very surprised if they specifically address the Amel installation, which is totally different than any conventional boat. Specifically and dramatically different is that there is no thrust component in an Amel, either fore or aft, which is the major force in any other installation. Amel installations present only torque. Also, the engine weight is not supported by (just) the four normal engine mounts, but is spread over six mounts (along with some "C" drive weight). I'll bet you dollars to donuts that no "specialty engine mount company" spec'd six engine mounts for a Beta to be installed in an Amel. It seems plausible the vibration issue may be connected with the old reused mounts that Amel specified for a much lighter engine, albeit with no thrust component.
Just another two cents!
Craig - SN68 Sangaris, Tropic Isle Harbor, FL