Thanks for the link. It really helped me in working out how to explain this exactly.
In music terms (recording artists), a "deep cut" is a track that doesn't get commercial airplay, and is generally ignored on an album. An obscure track (song/piece of music) in a musical artist's anthology.
We could have a guess at the meaning by looking at the end of the end of the sentence: "...not just the stuff everyone knows."
I guess the composer's plan is to "reward" the hardcore fans of the game by using the lesser-known pieces of music that only a hardcore player would know.