Lost in Space...
Verify tire width and pressure. I'd be surprised if there is that notable of a difference due to frame design.I realty felt every single bump in the road with this bike however so this may be a contributing factor to the discomfort. Hoping to ride it first tomorrow so I will have a better idea if it really is a harsh ride or if I was just getting tired.
Beyond that, I think you are way over thinking it. Personally, I can't stand disc brakes as I've had too many issues with them; I really don't see the advantage outside of racing.
If you think that having 105 gives you such a big advantage, you'll end up upgrading to ultegra in a year or two anyway... but I don't know, I haven't been following trends lately. Is 105 still the lowest 11speed setup? I guess that makes it worthwhile from the perspective of future upgrades and compatibility.