Yep, his choice has been discussed many times and is perfectly fine in THCD. Black shoes are always acceptable with the kilt, and some even say that black shoes are the only proper choice (although there are certainly plenty of examples of brown shoes being worn by traditional Highlanders). For daywear, either a brown or black sporran is perfectly fine, regardless of the shoe choice. Matching leather colours just doesn't seem to matter for daywear. Evening wear and formal wear are different, though. Black is the way to go.

As I recall, Charles's shoes are very old and are part of his personal style. The 'hunting' sporran he wears was passed down to him, and he wears it for the sake of tradition. Putting the two together is just fine, especially since they have meaning to him.

Or to rephrase the question: is there a right way to mix leather colors/textures? What are some suggestions?
I'm not sure there is a "right" or "wrong" way. Personally, I'll wear a brown sporran with black shoes but can't recall ever wanting to wear a black sporran with brown shoes. I do have a sporran that's two-tone black/brown, though, which I will wear with either colour shoes. I'm more interested in mixing interesting styles of sporrans and shoes rather than making the colours match, but that's just me.