In mfgtool release 1.0.0 I, "Support only Cortex-A5 as primary boot core (Cortex-M4 boot is not supported on this release)." When will a version supporting M4 boot first be available?
Mfg tool is based on it's counterpart, the ROM code. Rom code is for the A5 and not for the M4 as a matter of fact if you boot with the M4 and the device doesn't enumerate on the USB port at all then you know why and the MfgTool won't be able to do anything about it.
Currently there no plans to provide a MfgTool version that supports boot from M4 core. Customers can modify the exisiting code to make it work with M4 as primary core. Booting from USB with the M4 core should work. The image that is booted must be for execution on M4 (thumb mode).
MfgTool uses u-boot and a micro linux kernel to download images and program memories. This Linux can only run on the A5 core. To make it work with the M4 core as primary, it should be sufficient to add some code to the exisiting A5 images. Code will execute on M4 and start the A5 at the proper address as if it is booted from the A5.