Eh, if they're doing it for Half Life Alyx, it'll likely work like Proton, where Steam will automatically install a native version if it's available, and you can "force a compatibility tool" if you'd prefer to run the original version through FEX. Presumably any dev would be able to upload a native ARM version for Steam Frame/a hypothetical Steam Deck 2, but I imagine very few will.

Edit: Valve engineers pretty much confirmed this to Gamer's Nexus, as they described Steam automatically installing the best version for your device, and that you can manually override that.