It is in retrospect a pretty banal observation. If cipher design is about achieving a certain security level at the lowest cost per byte, it sort of stands to reason that you'd want to design them around those features of a CPU on which the market is going to put the most pressure to improve.

In fairness, some of this design philosophy --- which Bernstein has held for a very long time! --- gets a lot clearer with the advent of modern ARX ciphers, which dispense with a lot of black magic in earlier block cipher designs.

A really good paper to read here is the original Salsa20 paper, which explains operation-by-operation why Bernstein chose each component of the cipher.