I work in a Trek Concept shop with a bunch of other "bike people" who take pride in their work. Concept shops outside the Madison shops are Independent Dealers.

Your headset: when you say you hear a rattling, do you mean your headset is loosening up to the point that you have flex at the headset -- you're off your bike, you grab the front brake and try to rock it back and forth and you feel the bike move, with a click at the headset? Or, you're riding around, headset is tight, no handling issues and you hear rattling when going over bumps and the like?

With previous issues regarding Trek carbon steerer forks and issues working with carbon in general, I have a hard time believing the shop did not torque your headset/stem to spec. However, you are working with new technology and Di2 internal routing depends on zip ties around the wires to keep them from rattling around in the frame. Carbon frames are notorious for amplifying noise... Could just be the internal wiring needs a bit of futzing and maybe a few more zip ties to wedge it in place in the frame. If the fork is indeed losse, could be the carbon expansion plug used in place of a star nut to tension the bearings is slipping on assembly, but the shop should pick up on this.

Wheels come assembled, with tape, tubes, and tires installed. That was a factory issue. Did the shop charge you for the fix?

Crank falling off is an assembly issue on the part of the shop. The "cotter" the shop could be talking about is the safety tab in the slot at the end of the crank arm which should key into a matching hole on the crank spindle/axle. Sounds like they did not torque down the two bolts at the end of the crank.

Scratches on your bike while in for service is indeed a service issue...