While browsing around the Trek website I came across this PDF file, which states:
Some stems utilize designs that are not compatible with carbon steer tubes. Installing an incompatible stem can create a load point that can damage a steer tube, which may lead to a steer tube failure. Trek strongly recommends using a Bontrager stem with your fork. Bontrager stems have been designed and tested to be compatible with both aluminum and carbon steer tubes found on Bontrager forks. Installing another brand of stem could cause damage to the steer tube and will void the warranty of the fork.
The Domane 6 has a carbon steer tube. Trek did not send me a stem with it. I was planning on using the old Deda Newton stem from my 5200, or possibly getting a Zipp stem if I require a longer stem to make the bike fit. But after reading this PDF I'm curious as to why Trek would not send me a stem with the frame, knowing that I could void the warranty on the fork by running a non-Bontrager stem. I emailed them about it last week but so far I haven't heard back.