Hi Raymond
suggest to build just Uboot (not MFG) and try to boot it,
flash_header.S should be modified with new DCD settings.
Regarding MFG Tool, its firmware (initramfs.cpio.gz.uboot)
should be rebuilt with new DCD, please check
i.MX_6Dual6Quad_SABRE-SD_Linux_User's_Guide.pdf
sect.3.9 "Building Manufacturing Firmware".
L3.0.35_4.1.0_LINUX_DOCS 
Actually you can download just modified Uboot with MFG Tool,
modifiy ucl2.xml (also one can create new Profile, check with MFG2 Tool documentation).
u-boot-mx6q-sabresd_nopad.bin is Uboot image without offset (0x400).
Note, for USB loading one needs the same images, but without offset.
Changed "SabreSD-SD" profile:
<LIST name="SabreSD-SD" desc="USB SDP">
<CMD state="BootStrap" type="boot" body="BootStrap" file ="u-boot-mx6q-sabresd_nopad.bin" >Loading image</CMD>
<CMD state="BootStrap" type="jump" > Jumping to image. </CMD>
<CMD state="Updater" type="push" body="$ echo Load Complete!">Done</CMD>
</LIST>
On Windows platform for creating Uboot image without offset, "dd"
utility may be used (http://www.chrysocome.net/dd):
dd.exe if=u-boot-mx6q-sabresd.bin of=u-boot-mx6q-sabresd_nopad.bin bs=1024 skip=1
Best regards
chip