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The way we flashed new OPAL on machines in the lab was different than what may work externally, as they tend to be a bunch more locked down. You can look at things like external/boot-tests/fsp_support.sh in skiboot and the FSP/ASMI code in github.com/open-power/op-test for pointers.
It doesn't bypass the service processor, just works with it differently. It's a different bunch of code that gets loaded onto the POWER processor as it's Initial Program Load (IPL) and then gets to run an OS. You can even see the code in skiboot (OPAL) that talks to the FSP (Service Processor) in https://github.com/open-power/skiboot/tree/master/hw/fsp and related files.