I totally agree with you with the BB90. Given the option I would rather have a threaded BB just because it is such a tried and trued system. I also agree with you that the one bolt seatpost clamp can be a pain. I have found though that if torqued to spec they really do not move but getting the correct tilt is more work than it should be.
I feel like the Domane is brilliant in eating up the miles quickly. Absolutely no pedal bob at all. I have my slider set down one line softer from the middle setting. We do have some older riders on the SLR with the slider set all the way down and I can see a LOT of movement when they pedal but I have never heard them complain about it. It climbs well and I certainly cant detect any flex anywhere on the bike when hammering on it. It is not what I would call a fun spirited bike for me though. It is a bit to muted but then again that is what it was designed to do I guess. If I had the finances to own 2 high dollar bikes the Domane would be a keeper. As it is I have a 2018 Emonda SLR frameset on the way to me and I will be swapping everything over to it from the Domane on Monday. The Emonda is ALMOST as compliant as the Domane but the handling makes me smile everytime I ride one. I truly enjoy that bike and the fact that the frame is sub 650grams is just a bonus. I dont have near enough time on the Madone to have any real opinion that matters. Its a bike we SHOULD sell more of but we don't. Really no excuse for that. Here in SW Michigan the aero of the Madone should trump the light weight of the Emonda.

As a side note.... I did have a Roubaix SL4 for years before I had the Domane. I would have a real hard time if I had to pick one over the other.