The big concern is in multiplayer, where mouse and keyboard players could have advantages in some games (they can maneuver more quickly in shooters, for example). Microsoft would prefer that developers offer the choice of playing only against rivals with similar controllers, so players who can't or don't want to buy extra peripherals won't be at an automatic disadvantage. Also, support won't be mandatory. Ybarra says that's "based on developer interest."
To some extent Microsoft has already been experimenting with support between Gears of War 4 (where there have been mixed-input online playlists) and Minecraft's Better Together update (which has some mouse and keyboard functionality). However, it's difficult to say how well support will pan out once compatible games arrive in earnest. Will studios honor Microsoft's recommendations? And if they do, will they risk splitting the community? There's also the temptation to offer 'lazy' ports of PC games where the gamepad interface is almost an afterthought. It's likely that creators will accommodate both control methods in order to reach as many players as possible, but there could be some hiccups as producers get used to the concept.