it's just preference. I like to install some indie idles on my Steam Deck in desktop mode cuz then I can kinda just passively have an idle running.
Doing it this way would let me set up my own controls instead of having to modify the browser control set.
Edit: It also works in browser, but Fullscreen Chrome on the Deck is a little wonky at times. I think it's more Chrome on the deck than the game itself. Figured I'd add this info in, just in case it's useful.