The Sox also did have a A team in Burlington Iowa is the 90s, IIRC.
I've heard that the KC Cougars do not want a Chicago affiliation, as they don't want to alienate part of their potential attendees. I know if the Cougars were a Cub affiliate, I wouldn't want to support them. Personally, I'd love the Cougars to be a Sox affiliate, but I understand why KC doesn't want the Sox.
If the Sox can save money by having most of their affiliates in the same region, I don't have a problem with that. The way Kenny runs the minor leagues, we see very few of those players in Sox uniforms anyway.