Yep, it's all good. I believe I understand what Atmasphere was going for. However, I think for those in this upper end of the market the cost of an additional IC isn't that big of a deal. If a particular integrated sounds better than a particular set of separates, or if the separates sound better, is only an evaluation of those pieces. Extrapolating those results into some blanket statement about which approach is superior is great marketing.
T_bone, Nick has already done an excellent 2 chassis, full-function preamp with built-in phono stage. The 4 chassis model that I commissioned was exactly as you say, more expensive, however it does surpass the 2 chassis model in performance. (I even skipped the remote, to give an idea of what I am after.) The four chassis model is the separation of the pre and phono circuits and a separate power supply for each, 2 circuit chassis and two power supply chassis. There are always trade-offs and implementation is everything. The extra IC is not a problem at all from where I sit (pun intended). IMO, YMMV, and all that.
disclaimer: I don't represent Doshi Audio, I'm just a very happy camper.