That is an insightful question! A lot went into the notes. This game came together very fast so most of that was implemented in one day where I was collaborating with our musician Chris. I had to go back to look at the code to remember what it's doing XD
Basically all the score groups are sorted by length, so smaller groups score first. Each type of color and shape has a certain list of notes it can play when it gets scored. They're all from the same key. If it isn't the last score group, there is a little chance to add in a discordant note (which means it always feels resolved because the last group will always be harmonious).
There are also little randomizing factors that make it feel more dynamic. For instance a randomized time delay between notes played and a chance to play more notes at once and slight variations in volume as well. Chris also recorded a bunch of different variations of each note which helps it feel more natural.
I don't think people generally notice it consciously but I think having all that information and variation underlying the scoring (which is the only music in the game as you know) makes the game feel richer.
