by that BIOS programming isn't supported isn't that the MB isn't capable, but that MSI doesn't provide the specs for the flash programming interface,
The interface will be in the data sheet for the flash part. The only thing that may be MB specific is how to assert the write enable line on the flash. It may be hooked up to a GPIO or perhaps some sort of latch.
Do you have the factory flash app? If so then you can probally run it under dosemu and figure out what register they tweak to enable flash writes. Also Disable the shadow of the BIOS range and do a write to that range and see what the write line on the flash does. It might just be hooked up without anything fancy.
and that the BIOS programmer that comes with LinuxBIOS doesn't support my flash chip.
That should be pretty easily to fix. Most flash chips are very similar in the programming sequence. Get the data sheet for your part and fixup the flash code.
-- Richard A. Smith