I started a longer (12 mi ea way) commute this month and have been using both my cross/commuter (Bianchi Castro Valley) and my road bike (early 2000s Trek OCLV frame). Both bike have 23mm tires - Conti Gatorskins on the 'cross and Vitorria open Corsa EX front/Gatorskin (for now) rear. My average door-to-door times for the 2 bikes are within 5 minutes of each other - the road bike is slightly faster (and I tend to ride more spirited when using it). The 'cross has a rack, fenders, panniers instead of a backpack, a better light setup, and can take wider tires (35mm studded in winter) if weather or pavement required it. And I don't feel as badly leaving it out in the rain at the bike rack. I may get 25 or 28mm tires for the 'cross when the current set needs replacement if I want a slightly more comfortable ride.

I move wheels back & forth between the bikes, but prefer something closer to bomb-proof on a commuter. Especially as the distance goes up.

The 'cross would likely be almost as fast as the road bike if I stripped off all the commuter stuff and rode it as hard. In your case, I'd use a cross bike as a dedicated commuter and save the wear on the Madone; plus you can always use it on nice days and as a back up. A possible disadvantage of a cross bike are shorter chainstays = heel strike if you have large panniers (and larger feet). I've noticed toe overlap espeically with a front fender; this may be a function of a smaller frame size.

The other option for your situation may be a frame intended for radonneuring - more road-like than the cross bike, lighter than a tourer, designed for long-haul comfort over handling and able to carry some gear without getting twitchy.