Here is a potential solution
From emulationstation, enter RetroPie configuration Then RetroArch In the Main Menu of RetroArch, select Settings -> InputFrom there, go down to Port 1 Controls and update the following
Set Device Type to RetroPad with Analog Set Device index to 8BitDo SN30 Pro+I was able to get two controller working with this work around.
Versions
Program Version / Hash emulationstation 2.9.6RP retroarch-setup.sh b3acb001fcf6276a2ef5c5b4caca135b399797f8 retroarch 8373ac6In hindsight having a keyboard plugged in may have been problematic in regards to it defaulting to the primary controller.