I agree that a solidly mounted motor is probably the best way to keep vibration down. Other than vibration being uncomfortable for riding, it can also cause fuel to froth up in the carb and the motor will bog down or rev out of control due to too much air in the mix. I had this problem when I had a nuts on my motor mounts started to come loose once.
To keep it tight, be sure to use some thread locker on the bolts for the motor mounts. If you want to protect the paint, some inner tube rubber is a good idea, accept for one thing. If you can't mount the motor in such a way that allows both the front and back mounts to be totally flat on the frame, the mount that sits on edge will cut right through the rubber and dig into the frame. I also had that problem.
I got around that problem by using some heavy duty leather instead, around 1/8 inch. I think the leather does absorb some of the vibrations from the motor, but more importantly, I think it helps the motor mounts grip the frame a bit more tightly. It will compress and form to the mount, so that if the nuts do start to come loose, the motor won't shift as easily. I discovered this when the nuts on my mounts came a bit loose. I didn't think they had come loose till I looked at them since the motor still had hardly any side to side play in it.
The leather will also fill some space in a mount that won't sit flat, like the mount on the seat tube in my case.
That was far more long winded than I intended it to be

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