When PXE booting, /proc/mdstat doesn't exist, and the script in the initrd at /scripts/local-top/mdadm causes the boot to panic and fall to the initrd shell.
Removing /scripts/local-top/mdadm from the initrd (and it's reference in the ORDER file in the same directory), and re-making the initrd image allows successful PXE booting.
I don't know why /proc/mdstat doesn't exist when pxe booting, and I'm sure fixing that is the correct way to fix the problem, rather than my hacky "remove the mdadm" method above, and probably needs to be investigated by someone that understands the boot process more than I do.