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"