Is it possible to use IPMI to boot a cPCI server with a backplane? (in a similar fashion to Wake-on-LAN)?
IPMI is a network protocol. What it CAN do depends not only on it, but also on how it is implemented.
if you ahcve a BMC that is workng even if the computer is off AND it allows to power control the machine - yes. This is standard for any BMC I have ever seen, but some cheap out there may not support it.
Often you do not use IPMI even most of the time - you can use a website or some web services to start the machine, using the controller board.