In the case of a Di2 Madone 6.2, the majority of it is done in the bike shop, including torquing just about all the bolts that actually matter. But the rim tape would've been installed at the factory. Of your laundry list, the left crankarm falling off is the most concern. I imagine the assembler simply put the crank on and forgot to fasten it, with a torque wrench or otherwise, before moving on.

I work at a Trek dealership too. I don't see Trek's warranty department providing you any meaningful help here. They're not going to send a technician from Wisconson to your house to check the bike over. If you don't trust the store you bought from, ask around to find out which other local shops have a solid reputation dealing with high-end carbon.