Default You didn't read it carefully

Again: YOU HAVE TO DISTINGUISH BETWEEN OVERWRITE AND OVERRIDE. We all know that a file located in ROM never can be 'overwritten', but 'overridden', this due to the fact how WinCE searches for a DLL called by an application: 1 -> in directory where the application is located, 2 -> in folder \Windows, 3 -> in folder declared in CE's SystemPath and 4) finally in ROM.
Ending this excursion into the world of WinCE: If you make the desired DLL-copy-operations directly after device.exe (CE 5) / device.dll (CE 6) has done its job (means file system is mounted and ready to be used) you can 'override' each ROM-located DLL if it isn't already lasting (loaded) in RAM, means you simply copy new version of DLL to folder \Windows. BTW: The DLLs you see in [I]\Windows[I] might be located in ROM, or not ( i.e. located in RAM - folder [I]\Windows[I] itself is RAM), this depends on how OEM implemented this.

Only a practical example I've in use:

;increase storage memory (KB)
W \NandFlash\CE-Utilities\SetSystemMemoryDivisionKB.exe, 3072

; delay execution by the passed value in milliseconds
D 1000

;load backlight settings
W \NandFlash\CE-Utilities\regimp.exe, /f:\NandFlash\MyRegistry\backlight.ini /s
W \NandFlash\CE-Utilities\RegFlushKeys.exe

;prepare using .NET CF 3.5 instead .NET CF 2.0 (ROM located)
C "\NandFlash\NetCFCfg\device.config" "\Windows\device.config"
C "\NandFlash\MyCESystemPath\mscoree.dll" "\Windows\mscoree.dll"

; delay execution by the passed value in milliseconds
D 1000
Original ROM-located mscoree.dll (part of pre-installed .NET CF 2.0) gets overriden with mscoree.dll that comes with .NET CF 3.5, thus now .NET CF 3.5 is running instead of .NET CF 2.0