While investigating ways to implement the WinPE-SRT-Package manually I found I would have to do the work myself as I found nothing out in the wild. I came across the following issues:
"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 with peimg /targetpath..."
Digging into the registry I found this was because of 1 registry key. It's located here:
What is needed is to change InstRoot to the directory below your Windows directory.
So, to enable this to work you'll need to set InstRoot=X:\
Why does Microsoft do this? So you can use a WinPE install off a harddisk with all the associated expanded files as oppoesd to a large WinPE image.
At least, that's what I've figured :)