Just use Aurora IP core or something with similar functionality. You have 2 bidir links, one can be used for DRTIO, second for simple control protocol. >From one side you have some inputs that are repeated on the other side. You can run UART, SPI or whatever you want since it is transparent. I used it to galvanically isolate ADCs and DACs operating at high potential. 2 low cost FPGAs, 2 SFPs, fibre and I got equivalent of 2 SERDES chips connected together. The same link was used to configure the chips over SPI.
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