In the circuit (Arduinoboy I guess?), there is a microcontroller with software that filters out the MIDI SYNC messages and converts them to signals that the software on the Game Boy understands. In case of LSDj, that would be 8 pulses (=one byte) on the clock line while nanoloop expects the data line to toggle high/low with each MIDI clock.
For emulation, you need to implement this functionality. Just forwarding the MIDI bytes to the link port only works for mGB.

I'm attempting to emulate the MIDI to game boy sync using the TCPoke BGB support, but I don't really understand one thing: How does the circuit work? From what I'm guessing, the MIDI pins just get basically mapped to the link cable. So in theory, all I would have to do is take LoopBe1 and write a python script to send it to BGB's virtual link cable, but I think I'm completely wrong. Thoughts?