I think you should skip option 3 . Isn't that where problems started happening when doing the Colecovision controller ?
The real trouble with the "Super Arcade" line of products was that the three outputs had to serve consoles that used three different controller signal schemes. The Atari 2600/7800 controllers are just a box of switches. The classic CV uses the diode array to turn all signals into a 4 item binary code that's read by the console. And the Flashback uses a coded pulses, more like a modern controller.
My impression at this point is that the basic 5200 controller is from the "box of switches" camp, same as 2600 and 7800, just with more switches in the form of the matrix keypad. If that's the case, compatibility with Atari 2600/7800 is a simple pin re-direct with no possibility of craziness. The Sega Genesis controllers are interesting because they straddle the two techniques: the D-pad and fire buttons "B" and "C" are pure switches with dedicated wires in the DB-9 cable, while the "A" and any other buttons that might be present all share the remaining wires using coded signals. For this reason, our Seagull 78 is a glorified pin re-direct since we only wanted to move 7800 left and right buttons to Sega B and C. If my basic premise is correct about the CX-52, then a Genesis Aux-In would be no big deal.
Our engineer will be the one to tell us the whole story about how the CX-52 really works, and I am sure many of you know. If it DOES turn out that any "translation" is required, that feature will be dropped like a hot potato and the Super 52 will feature only the on-board controls.