I don't think that will happen. It'll be an option with each game. That's because what constitutes performance mode or graphics mode will be different for each game.
Well, yes - the idea is that you choose which one you prefer in general and the game applies its own performance / quality profile. That might be any number of variables like reducing resolution or detail for performance, turning on ray tracing and 4K for quality. Things that only mean something to the most hardcore PC nerds, like ambient occlusion, supersampling, temporal antialiasing, and so on.
Even if you have to go into the options to set it for each game, it's only going to be an A/B sort of thing. They won't show all those things to console players, so why not have it done centrally, via a setting in the OS? That way you never have to dig around under the hood.
I agree that they probably won't do it, because they had system-wide preferences on the 360 but abandoned them on the Xbox One. It was such a useful feature - you could choose all sorts of stuff, like how you want the controller set up in first-person games, whether you like in-car view and automatic gears in racing games, etc.
Also, I suppose if you don't realise you have performace mode turned on all the time, and they don't alert you when startung a game, you might wonder why your games don't look so good.