Got the batocera controls working. Select Amiga Keyboard in the controls option. Map the arrow keys to the joystick directions. Map south to Keyboard A, East to Keyboard W and R bumper to Keyboard D. Also Start to Keyboard 1 and Select to 5, for the credit and start button. DO NOT DO THIS IN THE BATOCERA FRONTEND! Do it in the puae control settings in the game in the retroarch in game menu. Remember to save your keymaps for this game and this game only! This works on a properly mapped 6 button joystick better than a controller. Finally have fun. A side note you will not be able to use cheats (you have infinite credits so don't worry). And you may have some trouble selecting the file (just move the cursor down a little and then up a little till the doubledragon file is highlighted).
What I described above seems to only be with DragonRise joysticks.
I have another machine that I tested the game on and it runs with only some sound and the joysticks on the machine have a xbox 360 joystick encoder. The controls behave fine. I believe the second machine I tested it is mono, so maybe the few sounds that did not come out need stereo?