I did what I think you're asking about with my '05 E350 EB that was formerly a wheelchair lift equipped Club Wagon configuration. I had greatly considered replacing all body side glass (except doors) with custom-made aluminum panels but formalizing my design or concepts left me frustrated for a million reasons, the main one being I'm so super anal it would have been difficult to do it to my satisfaction. Enough of my problems though........
Factory installed glass in that body configuration definitely requires access from the interior to remove/replace it. When you cover over the glass (as I did) you force yourself into removing whatever interior you've installed should any lite be broken. That might be something to consider before proceeding as it might affect your build out.
As my van is now the dark tinted factory glass is still in place but my build completely covers them with rigid foam insulation glued in place behind 0.090" commercial grade PVC panel sheeting covering that, affixed top and bottom to wood strips acting as firring material.
This works for me because is a work van full of tools so security is a concern---if they can't see it they might not think anything is inside--hopefully?
I also wanted every square inch of vertical and horizontal space be useful so "eliminating" all those interior glass surfaces became practical as well.
Do keep in mind my job is installing auto/truck glass.