Don't bother with flashing rootfs/eMMC. Just get it able to load and boot a kernel (using the clean-room reverese engineering I already suggested). From there, we can make minimal Linux builds that flash rootfs/eMMC over some standard protocol. So the process would be (all internal to the tool): load minimal-kernel, boot it, then have it reflash the rootfs/eMMC intelligently (it could even optionally preserve repartitioning, by formatting and mounting the target filesystem itself!).