Try with DISM:
https://msdn.microsoft.com/en-us/library/ff794819.aspx[EDIT]:
I did some tests, to apply the MS msu package with DISM you need to add some dirs/files from boot-wim-source to the boot-target (example for x86-source):
"\Windows\System32\catroot\{F750E6C3-38EE-11D1-85E5-00C04FC295EE}" -> just the directory seems to be needed
"\Windows\winsxs\Manifests\x86_microsoft-windows-classpnp_31bf3856ad364e35_6.1.7601.17514_none_178a98870a53ee4d.manifest"
"\Windows\winsxs\Manifests\x86_microsoft-windows-imagebasedsetup-media_31bf3856ad364e35_6.1.7601.17514_none_721540bbe51e7831.manifest"
"\Windows\winsxs\Manifests\x86_microsoft-windows-storport_31bf3856ad364e35_6.1.7601.17514_none_2983b8948e70fede.manifest"
"\Windows\winsxs\x86_microsoft-windows-classpnp_31bf3856ad364e35_6.1.7601.17514_none_178a98870a53ee4d\*.*"
"\Windows\winsxs\x86_microsoft-windows-imagebasedsetup-media_31bf3856ad364e35_6.1.7601.17514_none_721540bbe51e7831\*.*"
"\Windows\winsxs\x86_microsoft-windows-storport_31bf3856ad364e35_6.1.7601.17514_none_2983b8948e70fede\*.*"