Go with the purple Emonda. The level of ride comfort isn't going to be appreciably different between the two, quite honestly -- the Domane is just going to be more upright. That might make it more comfortable if you have back issues, but if you don't, it's just going to sit you up in the wind more. Your choice of tires, shorts, gloves, and shoes will have more to do with your all-day comfort than the marketing/geometry of the bike.

As you get into riding more, you'll get more fit, lose a bit of weight and be happy you bought the racier bike.

By the way, you can change the cassette to whatever you prefer/need -- in fact, if you're dropping coin on a new bike, ask the shop to change it for you. They should do so without question or extra charge.