Most organ MIDI conversions stop at output. Scan the keys, send Note On, done. The 555 project goes both directions because the organ already thinks in voltages and switch closures, and MIDI can generate both.
The 555's MIDI conversion reads keys two ways — shift registers for the authoritative on/off record, capacitive sensing for expression. The shift register wins every disagreement. That constraint is what makes the layered approach safe to attempt.