The better bike is the one that puts a bigger smile on your face.

I have a Helium and a Madone both rim brake and running SRAM red mechanical. I purchased both as frames and assembled myself. The Helium is significantly lighter than the Madone, it is also a few years older. I pretty much ride the Madone every time; it puts a bigger smile on my face. The Helium gets ridden when I expect higher winds. It just handles better in the wind.

With Trek, you can do Project 1, for a small fee, and select a different wheel set if that is a concern between the two.