Yeah too easy, it's just two batch files... you could have more for more setups. But in my case, I just wanted to either run in "VR" mode or "Steam" Mode.
Make a backup of your PinballX.ini file from the config folder, call it PinballX_Backup.ini.
Load up the Settings.exe program, and configure PinballX to your liking.
Copy the Pinball.INI File to what ever you wish to know it as, In my case I used a Steam.INI & VR.INI
Make sure your batch files have the right INI in the copy command
start_steam.bat
@ECHO OFF
CLS
CD C:\Games\PinballX\Config
DEL PinballX.ini
COPY Steam.ini PinballX.ini
CD C:\Games\PinballX\
pinballx.exe
start_vr.bat
@ECHO OFF
CLS
CD C:\Games\PinballX\Config
DEL PinballX.ini
COPY VR.ini PinballX.ini
CD C:\Games\PinballX\
pinballx.exe
I could have got more creative, but I was only after a quick solution and this worked.