While I agree with you, I think their take on it makes more sense if you look at it from a perspective of trying to represent as many diverse cultures globally as possible in a limited civ count, rather than looking at it as whether one civ of a pairing can 'represent' the other. For example, if devs can only fit, say, 50 civilizations into a game, they're probably not going to choose both Mali and Songhai, because that reduces the amount of slots available for civs elsewhere in the globe, including civs that may stand out more from others in terms of lifestyle, territory, etc.
That doesn't mean that Mali can represent / be a stand-in for Songhai, or vice versa. It just means that the devs want to cover as much of the globe as possible, and probably think that there are enough similarities between Mali or Songhai - or at least that there are other civs more distinct from one another than Mali and Songhai are - for it to make sense to only include one of them per game. Whether territory or general geographical location should be among the main criteria for choosing a civ is debatable, and whether the civs in each of these pairings should be considered mutually exclusive in a given game is VERY debatable, but I definitely think the devs are going that way with the civ choice and design: In V we had Songhai, in VI we have Mali. In V we had the Huns as the sort of steppe nomad civ, in VI we have Scythia as the steppe nomads. In V we had Denmark as the Viking-esque civ, in VI we have Norway as the Viking civ. If the devs included a much greater number of civs in the game, maybe such choices wouldn't need to be made, and there wouldn't need to be any implication of things as dubious as "Khmer and Vietnamese culture represent Siamese culture" if Khmer and Vietnam are in VI but Siam is not.
Of course, the person who brought it up presumably meant to imply that these cultures can somewhat represent each other, in which case what I just said doesn't apply and it becomes a complicated issue that I don't have the knowledge or expertise to make any comment on like you have. We've had many pages of such discussion in this thread already, as well as in other threads.