I don't know about the customer service aspect (someone else might), as you're mostly going to be dealing with the LBS. One thing I would check is the manufacturer's warranty on the frame. Ask the bike shop (if they're the same), since they should be able to give you a concise version or call Specialized or Cannondale directly. (The fine print is making my eyes glaze over.)
DBF, as much as he is a Cannondale fanboy (he'd marry his R2000 if it could cook), he'd probably tell you to go with Specialized; Cannondale's "thing", according to him, has historically been aluminum. However, that's his opinion, and the Synapse is probably a fine bike. I don't have direct experience with either bike--I'm researching for later. (Though, thanks for making me take a second look at the geometry chart for the Synapse. I may actually be able to make one work for me...)

I'm not sure you're going to get a straight answer on the carbon thing. What you're likely to get is a lot of marketing mumbo-jumbo dressed up with engineering terms.

Have/can you take them out on longer rides? They will probably feel very different, even though the fit may work for you.