@roslof Thanks! That may work. They'd just have to disable the port 3 and port 4 inputs if the 2600daptor selection were picked for the second port I guess. The suggestion I had was similar: have a core option "Paddle Type" for port 1 and port 2 that switches between unique controllers and 2600daptors. That's essentially how lr-vice handles inputs for Commodore 64.
An issue that is not yet resolved is the presence of one fire button per paddle. A single port would need an additional fire button in order for the 2600daptor to fully work.
You can update from source to test the latest if you'd like. It doesn't seem to affect anything else. Currently, the control types listed in the RetroArch Controls menu don't have any bearing on what happens in game. Stella's auto-detection still overrides that completely.
Speaking of the 2600daptors, have you tried mapping those in EmulationStation? I still need to go back and mark which paddle is which, but one moves the X-axis and the other the Y-axis of an analog stick according to ES. The two buttons are read as buttons 0 and 1. I am having trouble mapping via the EmulationStation GUI because of how the analog movements are read. I'm thinking I'll just have to manually map those in a config file. The lack of ES configuration means that the paddles don't get auto-configured when RetroArch launches. You can still map them in the RA menu while in game, and they'll work (very well), but we still need to figure out how to bridge that gap.