That and Open-top Tank Destroyers were not ideal for some of the urban fighting the U.S. did on their way into germany.
The advantages and disadvantages of open-top aren't even represented anyway, so there is zero difference in-game. If they were, then open top would have increased LOS (or at least vehicle detection) but be vulnerable to suppression (basically button fire from any unit?), gunfire from above (although the game engine doesn't see height), and explosions ('gunner shocked' from HE weapons?).
I think before WFA release, OKW functioned in a manner that required a lot of work to keep up in the game? But that mechanic was removed and the advantages remained. :/
That is true, originally you had to set up your trucks in a chain, the first connected to your HQ and the last hopefully on your Fuel. Only sectors with a truck on them gained 100% resources (went up to 200% but I don't remember the specifics) while the rest gave 33%. Your easy-access Panthers and Obersoldaten existed to protect that thin line at all costs.
If by "active" you mean "some supply planes" then you are 100% correct.
What if I told you that Luftwaffe strength was at it's peak in 1944?