I finally eliminated the loud cracking noise from my Roubaix Expert. In my case it turned out to be both the saddle clamp and the seat post clamp making noise, with the seat post clamp being the worst offender. I had correctly torqued both the saddle clamp and seat post clamp but was still having the cracking sound.
The saddle was moving backwards in the clamp during rides so I took it apart and found the powder coating on the saddle rails was being rubbed off. I cleaned all parts thoroughly with rubbing alcohol and lightly sanded the rails to remove all the powder coating where it mates with the clamp. I torqued it to 13.5Nm as recommended. That stopped the saddle movement and much of the noise, so that left the seat post as the remaining culprit.
I took the seat post out and found some dry film on both the post and in the seat tube. I cleaned that off with rubbing alcohol and then applied some carbon paste to both the seat post and inside the seat tube. After torquing to the recommended setting (6.2Nm) and doing several rides on rough gravel roads, I've not heard a single sound from the bike.
Additionally, I was skeptical of how accurate my torque wrench was so I bought the two Specialized torque wrenches. They have handwritten notes of the three tests they do on each wrench so I know they are accurate.
My bike was put together without using any carbon paste on the seat post / seat tube interface and correcting that, in addition to removing the powder coating from the seat rails, fixed the problem for me.