Very, very cool design and execution too!
Let me share an observation, by NO MEANS any bit of criticism at all!
The attachment to the door shell might be be streamlined a bit where threaded rivet nuts are installed into the door shell eliminating the need for bolts, nuts etc. Your idea of captive nuts between the MOLLE panel and door shell is outstanding---perhaps consider making those with a slip fit collar in place of the nut. From there the panels could be fixed in place with a bolt bearing one of your wingnuts or maybe a fluted round knob? You could somewhat reduce the amount of protrusion of the bolts and wingnuts.
If/when the MOLLE panels would be removed the original door shell smooth surface would immediately return.
Again just an idea but overall this is a very, very good idea!