With it being so close to the roof doesn't the sun's heat still absorb into the actual roof? The one I'm planning on putting up I was considering leaving about a 4 to 6 inch gap between the two "roofs"
Apparently not. It worked well enough in Saudi Arabia with temps above 120F daily. I'm sure if it's sitting still the heat will find it's way in through the walls and windows anyway. Also note that the sun shield is vented it's full length on both sides with tons of vent holes. This shield acts as any other object shielding the main roof from direct solar exposure would and this "shade" provides immediate and positive results, doesn't matter how far away it is, as long as air can circulate out from under it while stopped, and forced out while driving, the benefits will still be very positive. This solution was meant to enhance the ability of the A/C to keep up with solar gain coming from the exposed roof area, the moving air flow running lengthwise between the roof and sun shield while driving was a huge benefit. Remember that anything sticking up from the roof will eventually be found by passing trees, hotel canopies, low bridges, ad nauseam, pick another hazard and it will find exposed protuberances on the roof. This neat and low mounted sun shield worked wonders without exposing itself to passing hazards, engineered compromise comes to mind.
That's why I'm no big fan of adding anything above the original roof line without a really good reason, and an ability to absorb impacts without tearing holes in the roof. Also keep in mind that the attachment of said structure will most likely require the drilling and penetration of the roof, thus providing numerous entry points for water, and creating leaks that could be very destructive to the vehicle structure itself. I don't like the idea of drilling ANY holes in my precious vehicles, Anywhere, even the dash, since holes are forever and once made are never sealed or be made whole again.
Also keep in mind that if you do build a structure on your existing roof, especially 4-6" as you indicate, and most solar installations are even higher, I always cringe at them thinking of all the real world dangers lurking to take them out, that includes roof mounted A/C units, I'm not a fan of those either, for the same reasons. For me a smooth, unobstructed clean roof line is the goal. It's easy enough for stuff to hit and damage the roofs as built without adding further tempting targets for misadventure.
To each his own of course and I wish you well in making yours into the dream vehicle that works best for you. There is no wrong or correct answer to these questions, only the will and desires of the owner and how he intends to use it. As for me I have way too many years and miles in commercial service driving buses and trucks into nasty and sometimes dangerous situations to wish to make my own conversions anymore susceptible to the hazards of the real world and all the things reaching out and trying to damage my baby(ies), Crowns and this MC12