@chubbyrain The math tools we use are made for experiments conducted in the same context. Ideally they would query the presumed universal laws of nature and nothing else. When you test deck A vs B, even if no changes to the lists are made in the sample, then you'd still need to know that the players don't have different ways of playing the matchup. And there would be a multitude of parameters that could change in the sample A and B like their health, fatigue, etc. But we omit the human factors and still use the statisticians tools. If you test deck A vs the field you make the testing environment much more unstable, your field will change more than B, might be not representative of the "real" meta (not sure there's such a thing really :) ), and anyways the deck we face in a tournament are quite random.
Also on the personal level, I find matchup winrates, well, omiting that I'm not in favor on relying on stats in mtg, much more interesting for me personally. If I'm confident my deck beats X by a considerable margin, if I could have a relatively exact measure of that margin, I could use that as a tool to see how far I could go in weakening my deck a bit against X to help other matchups for instance. Since I don't expect to have reliable stats "ever" for tight matchups anyways, that's what I could use.
When playing against the field, I can try to use metagame shares (which are much more stable than winrates, or at least that seems clear to me) to chose decks and sideboard, but those aren't winrates, and also I base my strategy on the principle that only the players of top skill matter : if I'm not one of them I'll lose, if I am I'll win against the weaker players, so I'm interested in winrates against top players by top players, that's what of real strategical importance to me and by definition winrates against the field aren't of that nature. Sure neither are matchup rates typically, but they could be devised to be so, theoretically. (another reason why for me stats are so overrated in mtg)