My custom WINNT.SIF file has some options the Nlite doesn't give the ability to create. Here they are:

[Data]
Autopartition = 1

[Unattended]
Repartition = Yes

[SystemRestore]
DisableSR = 1
CreateFirstRunRp = 0

[Shell]
CustomDefaultThemeFile = "%WinDir%\Resources\Themes\black.theme"

all this options were talked here in this thread ....please search