Just to clarify, I am a trek sponsored athlete.
I want to chime in on this. I'm not a Trek sponsored athlete. I'm my own mechanic, and I wash my own bikes (when time allows). That being said, having the brake mounted under the BB is barely a chore, or inconvenience, and the aero benefits far outweigh any inconvenience. Actually, I have noticed that the brake stays cleaner than when it was mounted in the "traditional" mounting location, on the seatstays. The reason for this conclusion is that the brake is shielded from debris for most of the wheel's rotation (from the point of contact between the tire and the ground, the tire makes a 200deg revoltion (appx) before encountering the rear brake when in the traditional location, versus almost 300deg. when the brake is under the BB - the wheel almost makes a complete revolution). The only time I've encountered a problem is when I have had a flat, and sealant is spraying out. They're also protected from debris picked up by the front wheel because the Trek design places the brake far enough back on the BB that the angle of attack for the debris that could hit the brake is very small.
Now, are there drawbacks to the design? Yes. When I'm riding, I can't easily see if there's any rubbing going on with the pad. Also, changing brake pads isn't as easy (it also isn't THAT hard, just remove the pad holder, swap out the pads on the bench, and mount them back up - turns a 2 minute job into a 4 minute job). However, opening up the brake release is now MUCH easier, since it's located on the headtube, rather than on the brake itself. I can see where my hand is, rather than guess that my hand is reaching the correct spot.
Madone 9 https://goo.gl/7UwZpV
Madone 5 https://goo.gl/cMdyFo
Madone 4, SpeedConcept, Cobia
I own a lot of Treks.