Yes, that is a mystery. What is that mysterious pink wire, which apparently is terminating somewhere out of view at the bottom left of your picture? I'm also curious about that green wire which is connected to GND from seemingly out of nowhere on the top left.
That being said, I guess your best bet may be to just start pulling wires off and installing them into your new Rachio (congrats by the way). I recommend you connect the two white common wires to different C terminals (you have more than one) and don't forget to properly label (keep and eye on) the orange wire which is connected to the MV terminal (it will need to be connect to the M terminal of the Rachio), looks like you have a master valve so don't forget to enable it in the software.