Beats me on the margin on bikes but there are other manufacturers that at a similar price point will give you better name brand components and parts; Trek has a name in the business and so can charge a premium. You need to decide whether it is worth paying the premium.

Insofar as the bike is concerned, this is where the LBS matters. If you like one of your local shops and are getting good advice, I'd go with the bike the shop recommends.