You have described normal operation given the quality level bike you chose coupled with your weight. Don't worry about it. Unless you are making your living on the bike, it doesn't really matter. In my opinion, though, the wheels on such bikes are not designed to cope with that weight of rider. A pair of good strong wheels will minimize issues like broken spokes and dented rims, but don't expect magic.

By the way, I am a Trek dealer, so I know that bike well. The 2.3, at twice the price is more than twice the bike. That might well have been a far better option given you appear to like to ride fast. Better frame, fork, full 10sp 105 group, better wheels, yada yada....