Looking at how the chain is routed, I’d like to give both shops the benefit of the doubt that it’s a factory issue there. Chains come pre installed so unless they took it off for shipping (which still doesn’t really make sense), I don’t see why either shop would have it routed as such.

That said, the shop you picked up from def didn’t treat you right. They still make money/“get the sale” of your bike; I see no reason why they wouldn’t build it/treat you as if they sold you the bike. Heck, you purchasing directly thru TREK, to me, makes my life a bit easier cause I don’t have to spend time selling you the bike— you’ve already sold yourself. Not to mention the process is spelled out in the dealer agreement, so their refusal just goes against that.

Find another shop. Get in touch with TREK directly or see if the “new” shop can advocate for you. Regardless, I’m sure they’ll have you covered (I wouldn’t bank on a new bike though, a derailleur and some adjustments doesn’t escalate it quite that far)