EDIT: Adding some weird thinking... So if the soft rubber grommets are too soft, and as I tighten the nuts, the rubber compresses and I don't "feel" the spec'd torque amount, so I keep tighening. With the stiffer style grommets, they don't compress and when tightening the nuts, I can "feel" them getting tight against the cover and nuts. Does that make sense?
I'm sort of jumping into this discussion without reading everything, but it sounds like the speculation is that you're getting noise because you over tightened some bolts that eliminated the required clearance with internal parts. My thought while reading some of the posts was what I think you're getting at here. If the grommets failed while being tightened they would allow more compression and you wouldn't be able to achieve the same torque with the expect cover clearance.
Maybe Chris is correct for what's causing the noise, but instead of it being an issue of over tightening the bolts is an issue of the grommets failing as they were tightened.
