Here is a potential solutionFrom emulationstation, enter RetroPie configuration Then RetroArch In the Main Menu of RetroArch, select Settings -> Input
From there, go down to Port 1 Controls and update the followingSet 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.
VersionsProgram Version / Hash emulationstation 2.9.6RP retroarch-setup.sh b3acb001fcf6276a2ef5c5b4caca135b399797f8 retroarch 8373ac6
In hindsight having a keyboard plugged in may have been problematic in regards to it defaulting to the primary controller.