The stiffer polyurethane mounts allow the rest of chassis then to suspension and tires to ground to dampen the vibration from the rough idle. So its not rattling motor/trans as much.
This sounds like gear rattle internal to the transmission, between the input shaft and the countershaft immediately inside the gearbox. When you're in neutral, the countershaft is essentially free-floating in the rotational sense. The input shaft, on the other hand, is not rotating at a truly constant velocity (it speeds up and slows down as cylinders fire and you get a pause before the next cylinder fires). Clearance between the teeth on those mating gears allows the countershaft to go in and out of contact with both the drive side and the coast side of the engaged teeth on the input shaft gear.I have a 2008 GT 4.6 L I just put the Hot Rod cams in and mine does it too. I am glad to see others experience this because I thought I may have to replace my clutch!