I've found a few options, but don't know if any will work:
fastboot oem off-mode-charge 0 (doesn't do anything when I try)
https://www.olimex.com/forum/index.php?topic=1091.0 <- seems to be based on the specific hardware.
Modify init.rc (doesn't seem to work on other forum threads).
I'm worried we'll have to modify the boot-loader, but hopefully something can be done at the OS level.
If anyone has any hints I have a semi-disposable device so I'm not too worried about bricking. Also, if this is a big task but you can do it we can pay a bounty.