There shouldn't be any special reason for mounting the controller inside the fender except that it was probably easy to put it there, when the cars were assembled. (I'm guessing that all the mechanicals and wiring were installed before the body panels.) They already had wiring for the horns in that location, so it was probably just as easy to put the controller in the same general vicinity.
As for the flush mounts... There should be no need for any of the controller wiring. You should be able to just unpin it from the harness and remove it. Unless one of the controller wires was re-purposed for the headlights themselves, but I doubt that.
That is, unless you plan to go back with the pop ups.
Don installed the later harness and actuators in his car, I believe. I think he said it was completely plug and play.
John Champagne has also installed early harnesses and actuators in 87/88 cars, when the 87/88 motors were a rare commodity and the earlier pieces were plentiful. Said it was totally plug and play.
Scott... I might be interested, but not just now.