Carbon fork and frame for rough road

Don't worry, they'll be fine.
Decent tyres and the right pressures will sort you out.
Run something above a 25

The Domane 2 series are very good on 'normal' rough roads. The back-end really is excellent and makes a big difference whilst the front pretty good, but feels relatively less so due to comparison with the back - in reality it's a decent unit by any standard. For an aluminium frame, the ride is very, very good.

That said, I agree with the others that tyres make a huge difference, and IMO the Domane frame should take at least 28mm tyres - i've had Open Pave 25mm on Bontrager 23mm rims on one, where they measure 27mm wall-to-wall, and there seems to be a fair bit of room left.

I'd have thought that your 'average' CX frame would be a good deal stiffer, doubtful anything like as compliant at the back, but you could go up significantly on the tyre size over the Domane (or any of the road bikes) - at that point it's more a balance of comfort vs. tyre weight and ride.. 33-35mm tyres could give you a sublime ride over the chatter, whilst something like the Domanes IsoSpeed (or the VCLS seatpost from what i've heard) will give you excellent isolation from the larger knocks.

A CX bike also gives you the option of a bit more fun off-road should you want to play around with different tyre types but i'd also recommend the Domane highly.

I would agree with CXR, it is all about the tyres. I ride on some pretty s**t roads on a cyclo-cross bike with 28mm Specialized tyres with no problems. Whereas on 23mm tyres you lose the will to live, the difference is pretty dramatic.

Well, I hear Trek has a good warranty

A couple of suggestions - you might prefer a fork with an alloy steerer tube, since lots (majority?) of fork failures occur when the carbon steerer snaps (including high-end Treks). You can Google this - Trek recalled some forks and also prescribed only ever using the original stem, etc. etc. I'm sure it's not just a Trek issue.

Alloy steerer tubes are a lot more forgiving (and more common on the lower end bikes you mention) but do have the possibility of separation at the fork crown. I've not heard of one failing in that spectacular carbonesque way, though.

And you might run larger tyres. Not cyclocross wide, but at least 25mm or even 28mm as you can run lower pressures and absorb shocks better. So check the clearance on the frame for wider tyres.

Cyclocross is a road bike, more capable of taking rough roads, wider selection of tyres are available usually upto 38mm wide

Buy what you like but a road bike will generally limit you to 25mm wide tyres.

Buy a cyclocross carbon bike, use 35mm tyres to soak up impacts