I also think it could be because, as a triathlete, I spend about 1/2 of my riding time and the majority of my "quality" riding time in a very forward position on my TT bike. So my road bike fit might have me slightly more forward over the BB than normal as I feel more powerful in this forward position. On my Canyon, my saddle is basicly as far forward as it will go (as also run a stub nose Power saddle). I was initially set up with the saddle about 2 cm further back and running the 100cm stem that came with the bike and it felt like I was sitting in a recliner. I don't recal how it impacted handling really.
What I do find perplexing though, is why the Ultimate and the Palace handle so differently despite the contact points being quite similar. Looking at my VeloAngle sheets, position over the BB is the same, but handlebars are ~1cm lower and 1cm longer on the Palace:R.
With respect to the Aeroad, I'm going to try lowering the Palace another 1cm, to approximate the lower riding position of the Aeroad for a couple weeks and see how that goes. It does seem like I feel more in control of the bike with the Palace's lower riding position eventhough according to people here, that shouldn't really have any bearing on handling.