Chief wouldn't ally himself with the outer colonies simply because of his origins. Chief has never shown any interest in his childhood home and we've never seen his political views to my knowledge (if this has come up in any other media please let me know). Chief strikes me as a person who is about saving everyone (not just humanity), and doesn't necessarily care about political differences between the two groups. From these audio logs it looks like Chief isn't allied with either group and has a larger goal in mind. There is definitely a larger picture that Chief is seeing and is a part of.