Very cool, this is exactly what I was looking for to answer the how question.
These projects look awesome, if I'm ever in the UK I'll checkout their museum.
I've visited this museum and it was the highlight of my trip to the netherlands. I also wondered, for hours, about how cool it is to hook up modern hardware to these old systems. Can you imagine playing one live, similar to how an artist would play a synthesizer kit?
This would play MIDI files, not MP3s. Midi files are the digital version of that book with the punched holes, it's a sequence of note events over time.
The physical book with holes forms a series of air valves. So what you do to convert it is attach a bunch of pneumatic solenoid valves instead. Then there is some interface board that lets you control a bunch of solenoids from a laptop. It's not really that complicated but you need one valve for each note, so you need a lot of them, and you have to physically plumb in each one to the organ.
Have a look at Look Mum No Computer, he does this kind of stuff: https://www.lookmumnocomputer.com/projects#/joans-church-org...