Como consegui:
Suponho que eu poderia ter feito isso na imagem principal sem ter que exportar cada um individualmente e importá-los.
imagex.exe /export C:\Users\administrator.INTERNAL\Desktop\install1.wim 1 C:\Users\administrator.INTERNAL\Desktop\install2016.wim "Windows Server 2016 Standard Core" /compress maximum
imagex.exe /export C:\Users\administrator.INTERNAL\Desktop\install2.wim 1 C:\Users\administrator.INTERNAL\Desktop\install2016.wim "Windows Server 2016 Standard" /compress maximum
imagex.exe /export C:\Users\administrator.INTERNAL\Desktop\install3.wim 1 C:\Users\administrator.INTERNAL\Desktop\install2016.wim "Windows Server 2016 Standard 2" /compress maximum
imagex.exe /export C:\Users\administrator.INTERNAL\Desktop\install4.wim 1 C:\Users\administrator.INTERNAL\Desktop\install2016.wim "Windows Server 2016 Datacenter Core" /compress maximum
imagex.exe /export C:\Users\administrator.INTERNAL\Desktop\install5.wim 1 C:\Users\administrator.INTERNAL\Desktop\install2016.wim "Windows Server 2016 Datacenter" /compress maximum
imagex.exe /export C:\Users\administrator.INTERNAL\Desktop\install6.wim 1 C:\Users\administrator.INTERNAL\Desktop\install2016.wim "Windows Server 2016 Datacenter 2" /compress maximum