I found a solution!!!
For anyone who also wants to use a 3 button Sega controller, there is an option in the Retroarch menu under Settings—>Input—>Menu Toggle Gamepad Combo. You can set it to Hold Start for 2 seconds to bring up the Retroarch menu.
I’m still waiting on my controllers to be delivered, but I would imagine that I’ll also need to edit the Recalbox controller config file to remove the Hotkey from my 3 button Sega controller.
Edit: I just tested this on another controller and it works perfectly! I set the “Hold Start for 2 Seconds” to return to menu option. I then edited the Emulation Station input config file and set the “Hotkey” button to a number higher than my controller had. I found that if I removed the Hotkey completely, Recalbox would then ask me to reconfigure the controller.
I hope this helps someone!