I think AtariAge has had one up for weeks for rewiring the pinout to match the Colecovision's pinout. So it would be a trivial matter to apply this knowledge to a CX40 equivalent (And if it was an adapter like I think someone at AA is producing for the Intellivision model, it would be plug and play with Atari joysticks without any modification necessary).
The key question is if controller 2's keypad can be used to get a single player game going while using controller 1 to actually play the game with, like could be done with Coleco published software on the real deal.
If you have to start your game with controller 1's keypad, the value is defeated by the hassle of quickly changing controllers out (Although those really desperate could still come up with a solution).
Seems a shame, it's almost like they intentionally tried to not make these compatible. Even the overlays aren't compatible with the originals on at least one of the two new Flashbacks.