@mrjpaxton
The setup is 5 disk RAID6 for 'cold' storage (with ~20 minute disk spin down) that I access rarely, and a 'hot' SSD to store downloads, temp files, and anything that's not OS related.
The OS should be separated from this (previously it was on MMC, but as I did not have a backup, I lost access due to something and had to reflash, thus losing all config)
Regarding the other boot option, Neither HDDs or SSD should not have any boot related files, just data.
As for the main question of why it's plugged in in the first place, I use the USB header for the front panel for an internal SSD, but as the board's SSD slot can't be used if you use all 5 disks, this was the best workaround I could find. I would really prefer to boot from SD, as I don't know the expected life of the eMMC, and how badly I may have abused it, so it's safer to expect SD card to fail and plan accordingly.
SD Card is UHS Class 3, and I am not doing anything that should need high IO for the OS.