Prevent Windows System %PATH% from being prepended to user %PATH?

If you only need this to work for command prompt sessions, create a profile/init batch file and configure it in the registry, per https://stackoverflow.com/questions/17404165/how-to-run-a-command-on-command-prompt-startup-in-windows. E.g.,

reg add "HKCU\Software\Microsoft\Command Processor" /v AutoRun ^
  /t REG_EXPAND_SZ /d "%"USERPROFILE"%\init.cmd" /f

Then simply make modifications to the PATH in that batch file. E.g.,

SET USER_PATH=c:\whatever
SET PATH=%USER_PATH%;%PATH%