No, that's not where to run it. The batch file is for skipping the hardware checks when doing a clean install. Copy the batch file to you install usb so you have it handy.
When you boot from the install usb to do a clean install, at the first Setup screen press Shift+F10 to open a command prompt. This is an Administrator command prompt, so you can run the .bat file from it, you should find the install usb is drive D: after you have booted from it. After you have run it you can carry on with installing Windows 11 and it will skip all hardware checks.