Update 11/3/22: It seems Valve has updated the patch notes to include this. It was not in the original posting, but it is there now on Steam!
I definitely didn't expect to see this option available, but hot damn. Valve's last Client Beta update seemed to do forget one little addition in their changelog...being able to swap your A and B buttons to match the Nintendo Switch, as well as the X and Y! This means that your A button will react as if you are pressing the B button and vice versa when enabled. This does happen immediately and translates over to games as well!
To enter the Steam Deck Client Beta, go to your System settings > Steam Client Update Channel > then choose Steam Deck Beta.
In our testing, this will also swap whatever is assigned to those buttons in your controller configurations. So, if you are playing a game using a custom controller configuration where the Spacebar is set to the A button and Ctrl is set to B, if the Nintendo layout is enabled, these will be swapped! Still, if you are someone coming over to the Deck from a Switch, or just use the Switch a lot, this could make things significantly easier!