Not 100% sure if we've given that any thorough testing, but the ops team is looking at most available options before building these out. That said, if they haven't tried it, they'll read this and give it a go :)
Another option -- check out the very low profile USB thumbdrives (the one I've got sticks out about 4mm or so). Or see if you can get motherboards with an internal USB or SD socket. Maybe combine this with PXE boot for initial setup (the pod gets built with a blank internal thumbdrive, and on first boot it installs the Linux kernel and initial ramdisk image on the thumbdrive).
Edit: It looks like the motherboard you use does have a USB header on the motherboard, where you can plug in a boot thumbdrive.
Supermicro also sells a sata plug mounted storage device it would have enough for a kernel to be loaded.
though i think a PXE or similar boot option would be a smarter move. just enough to bootstrap something to run in ram. (alternatively a minimal kernel and dedicate a section of the disks in the chassis to holding the running software (500MB x 45 with decent levels of erasure coding is a fairly minimal slice.) the kernel could then pull down the code after first boot (or updates)