R7 builds the insole integrated with the last. Meaning that there is no separate insole. The thin foam foot liner is laid in over the carbon sole shaped to your foot, with the appropriate arches formed in the carbon sole itself. In my 3 pairs over the years (2 new, 1 used) I never found them to be too high or too low.
Whereas Don Lamson builds D2 with a flattish carbon sole, and a separate "orthotic" insole. Those orthotics were always too high for my feet, and he made them that way despite my protestations, saying I'd get used to it. I never did, and put in Superfeet.
You just summed up 2 very different shoe design philosophies quite nicely. I don't have experience with these 2 brands, but even within "off the shelf" premium shoe brands, you see a big variation, where some will have a nearly flat last that provides a kind of neutral platform for your preferred orthotic/ergonomic insole system, whereas others have a dramatically contoured last with a big molded carbon arch support. From an efficiency and weight savings standpoint, I love the idea of having the orthotic/insole integrated into the sole of the shoe, and if the company really can nail it on the first try, that's awesome. But from my experience with both custom molded corrective orthotics and customizable ergonomic insoles like G8s, besides the science, there is a bit of an art and also some trial and error involved in getting them right. The idea of having a whole shoe locked into a possibly incorrect configuration is a bit of a bummer.
I've always thought it would be cool if you already had some orthotics that you like, then you could use them as a basis for the shoe mold, which would take some of the uncertainty out of it as you wouldn't be trying to reinvent the (orthotic) wheel. I think that is what Adam Hansen does with his shoes, but it doesn't quite jibe with the whole crushbox foot mold system that most custom shoe companies use. You'd need to make a plaster mold of your foot sitting on the orthotic instead.