Do try to test ride the 2 bikes before making your choice. I tested both of them not so long ago, and I personally had a preference for the Trek one, although the saddle felt horrible, but the shop at the time was OK to swap it. The Scott felt more agressive, and I was fearing when trying it a lack of comfort on longer term. Now, we all have a different physiognomy, and my opinion is based on a 15 minutes ride only.
As for the groupset, even Shimano themselves will agree that they are very little differences. I remember watching a video of an EU Shimano representative admitting that the 105 and Ultegra are exactly the same in terms of dimensions and design. The only thing that changes are the manufacturing process and materials making the Ultegra a bit lighter. The overall quality of both is the same, and you shouldn't sacrifice comfort over a fancier label.