Windows PE cannot start because the actual SYSTEMROOT directory (X:\Windows) is different from the configured one (X:\$windows.~bt\Windows). This can be configured from dism.exe with the /set-targetpath command. Please consult the documentation for more details.
Press the OK button or close this message to reboot.
copype amd64 D:\Sources\OS\BootFiles\amd64
Here is an example of what it will look like as it extracts:
The boot.wim file will be located under x86\media\sources for the respective operating system architecture you extracted, as shown in the following screenshot:
If you use the boot.wim files from the Deployment and Imaging Tools you will not experience this problem and with any luck, PXE clients should boot straight into the SCCM configuration screen.
Make sure you don't forget to Distribute the boot images and update the distribution points.
Note: Make sure you restart the Windows Deployment Services Server service after changing boot files.