In the last 4 years I've taken 6 different bikes to work. 3 steel road bikes, 1 aluminum/carbon road bike and 2 rigid framed steel MTBs from the 90's.

The smoothest riding road bike is a steel Univega with a touring geometry. It has really long chain stays. The worst riding road bike? Also steel. The MTBs are a different animal except that one is a Bianchi that takes 700c wheels. This has allowed me to do some mixing and matching of tires and wheels between the Bianchi MTB and my current road bike which I did just for fun. The Bianchi has also undergone a drop bar conversion. So for about $200 total, I've gotten a nice double-butted cromoly framed bike not all that different from a Crosscheck in terms of it's versatility. It can take even wider tires than a Crosscheck.

Anyway with the same wheels and tires, I can't honestly say which gives the better ride, the steel Bianchi, or the aluminum/carbon Specialized.

So while I think it's great that the OP has found a bike/route combination that makes his commute more pleasant, I'd be careful about attributing that to frame material. In my experience, tires and geometry have made more of a difference.