@Arek-Z I modified the bootloader on an omega2s+, based on the github repo of onion. This went fine without problems. For flashing, I use a FTDI SPI cable in combination with the most recent version of flashrom, which works out of the box. You can freely write the flash as long as you keep the processor in reset, so unbricking is not a problem and all required HW signals are available on the omega2s. Just make sure that you don't erase the second partition, I don't think you can restore that one.
In practical terms, I added a programming header that contains the SPI signals as well as ground, 3V3 and reset. When the programming header is inserted, a short keeps the processor in reset, so that the flash can be safely programmed. This method only works with the s/s+ version of the omega.