good question, I would of said any bike, set up correctly, and fit to you, should be equally comfortable. I believe a true cross bike might have a bit less give in it thus giving a harsher ride.
My commuter is based on the Surly Crosscheck frame, I don't know if this is a true cross bike or not. Quite honestly I still get confused about what frame qualifies as what. I can say that, coupled with a Brooks B17 saddle, it provides a very comfortable ride for my 40 miles roundtrip commute. The only drawback is that it's a very heavy bike, 36lbs unladen. But it has touring rims, 35mm M+ tyres(these weigh nearly 1kg each), a hub gear(this weighs in at over 2.5kg), guards and a rack.
That said I've had no problems in nearly 1700 miles on it and it was chosen for year round conditions. If I could spec a new commuter it would basically be the same but replace the SRAM 9 speed hub with the Rohloff 14 speed, mainly as the Rohloff is 1kg lighter. I'd also have the same sort of frame but in lightweight titanium or top end 953 steel. As for the rest, I don't want wheels going out of true and punctures, low maintenance commuter is the purpose.