I believe WinPython Powershell Prompt.exe is just a thin wrapper around the batch file scripts\WinPython_Interpreter_PS.bat, which in turn calls the Powershell script scripts\WinPython_PS_Prompt.ps1 to set up the environment. As such, any arguments that you pass don't reach Powershell at all. Instead, arguments to WinPython Powershell Prompt.exe would probably need to be handled by both the batch file and the Powershell script that's being used. I'm not a regular batch/Powershell user, so I don't know if it's possible or even desirable to modify the batch and Powershell scripts to handle pass-through arguments.

Assuming that you're trying to script this rather than manually invoke your script within Powershell, the easiest workaround may be to create a Powershell script that first calls the WinPython Powershell script and then your Powershell script.