I suspect that the occasional Trek has a badly machined BB90 bearing bed - that is the bearings are not exactly perfectly longitudinal so when you press in the bearings in they are slightly tilted to one another. This is sure to cause a problem like that. It must be rare though since complaints are few and far between. I have a 2012 Madone and a 2018 Emonda that aren't put together yet how to not have any such problems.
Since the Madone is a 6.9, it is an aero bike and it is NOT set up for Di2 and requires an external battery and a couple of special Trek parts where you have to drill a hole and insert them in order to get the internal wiring. This is a bit discouraging since the same year 6.2 is designed to take Di2.