This is not a "stance", Microsoft owns plenty of game studios which are more than happy to include in-app purchases for every skin, emoji, and loot box they can.
They are preventing this for the reason others have already mentioned: they don't get a piece of the action.
Should be noted, Minecraft already allows Java server owners to take a surprisingly large piece of the pie. They've loosened the EULA to allow most forms of pay-to-win, you can pretty much sell whatever you want as long as it's not the specific narrow situation of items/commands that benefit a player's ability to PVP, used on a server that is almost exclusively dedicated towards competitive PVP. Other than that it's free reign and there's quite a lot of shady pay-to-win servers out there. (There are many ways to "win" in the game other than PVP, such as digging a massive hole -- no kidding, on our homely non-profit server we do competitive hole-digging and take it VERY seriously and would be pissed if someone was able to purchase an advantage.)
I agree with the feeling of being annoyed by pay to win. But I don’t think that Microsoft should be dictating what players can and cannot do on private servers.