I can't say for sure because I've never actually seen anyone do the "mud flap bushing", but I don't think that particular setup would work very well. Two reasons I can think of:
1. The bolts will be tightened down on the metal on top and bottom (the roll cage, and the tie-in), so even though the tie-in itself might not transfer as much vibration, the bolts certainly will.
2. The sandwhiching (a nerw word?) of the rubber, I think, will be too thin of a flexible barrier to absorb the flex.
Now, not one to be a naysayer of good ol' redneck fabrication, here is what I think you could do to make the mud flap idea work better:
1. Use more than one layer in the sandwhich between the three metal parts. So from top to botom, you'd have cage|rubber|body|rubber|tie-in. And maybe even double up on the pieces of rubber to give you +/- 1/2" of flexible material.
2. Use more pieces of the mud flap to isolate the bolts from the cage and tie-in floor plates. You could either make small rubber washers for each bolt, or just cut a strip for the front two bolts and a stipe for the rear two.
So the final sandwhich would look like this:
bolt head|metal washer|rubber|cage floor plate|rubber|rubber|body|rubber|rubber|Tie-in plate|rubber|metal washer|nut
Damn, I feel like a regular redneck engineer now! ;D