I'm with the OP on this one. A limit screw not doing its job almost always shows when you shift or apply power, not pedaling lightly. Cross chaining usually helps pull the derailleur outboard toward the outer chainring and away from the wheel.

Perhaps the OP is lying to us, the shop and therefor Cannondale. I'm sure that has happened. Or the OP is telling us straight up and Cannondale is appearing to not be honoring their warranty. They could have at least sent out a rep to look at it. Since the hanger is still straight, it should be possible to remount the wheel, jig the hanger in place and see if that screw is adjusted right. Yes? Offer a replacement. No? Show the mock-up to the OP and work with him to get things right. It's called customer service (or the customer is always right). I am guessing Cannondale can afford it, even in these tough times.

There was no danger of me ever buying a Cannondale, but they just slipped a notch in my book and someone else might hear of this incident from me.

Edit: and again, if the OP is telling the truth, that only the Cannondale authorized shop has touched the RD setup and adjustment and sent out a customer on a bike that will self destruct if he cross-chains? That's a big oops. If that happened, the shop should man up, replace everything needed and do it with a smile. And give a talking to that employee so it doesn't happen again. And the rest,, ie the dollar trail, is between the shop and Cannondale. The OP should see none of that.

Ben