I work at a Japanese institution which has a Tokyo-based international finance team. We are another example of a company that says "group X should be in economy, group Y should be in business, group Z should be in first, but any flexible fare is OK."

Most people seem to stick with FF programs that get them "home" easily - so locals use JL or NH, Americans use UA or DL, Canadians use AC, Brits use BA or VS, Europeans use LH or AF, etc., and then people work out ways to get their flying into the alliance of their preferred carrier. All three alliances have pretty decent coverage out of Tokyo in every direction, so it isn't too difficult. If we were in HKG, FRA, DXB or another city where the market is more monopolized, there would probably be more favoritism for the local airline, just for the sake of getting around easily.