Valve isn't burning any bridges here because there were no bridges to begin with.
Portal and Portal 2 recently released on the Switch
The only thing I can see this threatening is native JoyCon/Pro Controller support on Steam (more specifically use of their controller glyphs) if Nintendo want to get real vindictive. Otherwise there doesn't appear to be much of an existing relationship to be threatened.
Putting Yuzu into marketing materials was definitely a bit of a faux pas, but it's also one of those occasions that highlights the absurd pageantry of pushing the narrative that emulation is taboo. It's in the video because there are those at Valve use Yuzu on Steam Deck themselves and normalizing that is a net good.
I've seen a lot of formerly xbox and playstation exclusive titles start popping up on Steam... so you wouldn't need an emulator for those...
No other way to get Mario on Steam yet though ;)