Agree with Beaker, if the price is close, I would get the 3.1. They both have 105 shifters and RD. The 3.1 has a Tiagra FD but that is not significant IMHO. They both have Tiagra cassettes...again not significant. The brakes will not hold you back either. Like Beaker said, if your OCD tell's you to go for a matching group just upgrade a few things down the line.

Is Trek the only bike the shop stocks? Did you try any other bikes?