Just a follow-up for anyone experiencing similar issues:
I downgraded my 20TB to a 10TB so I could repurpose the 20TB into one of my NAS's and the warm-boot issue reappeared: this time with the 10TB, which was installed on the top slot formerly hosting the 20TB.
I switched the 16TB to the top slot and 10TB to the "middle" slot on the Flex cage and the warm-boot issue was resolved.
So my take away is this: the largest capacity drive should be installed in the top slot. This equates to internal SATA port 2 if the cable bundle order is manufactured the same as that which came with my Flex cage:
If not, or you are using a different aftermarket kit, then just ensure the largest capacity drive is connected to SATA port 2.