I think that at some point, firmware versions have been mismatched on-device.

Using the PR_LEGACY 006 firmware, add "--flash-only=rootfs" to the end of that command line, and on the second run to flash the eMMC, remember to have "--flash-only=emmc".

Don't reboot yet.

Now download the PR1.3 PR_LEGACY 280 rootfs, and "--flash-only=cmt-mcusw".

You should now have a device with PR1.3 006 on the APU, and PR1.3 280 on the MCU (and the MCU's swcert should match with the MCU firmware)

(IIRC mismatching APU and MCU firmware is allowed. In case you get a MALF, flash the PR1.3 Open Mode kernel and follow these instructions)