Steam OS is using Proton for translating/emulating windows apps, I know that even AAA games are working great with it but native binary is just straight better, and there always can be some possible issues or restrictions with Proton.
To be able to properly (or safely) use SteamAPI (like virtual keyboard) or SteamDeck specific controls Linux build will be most likely required.
Next thing is that other companies may use SteamOS for their handheld devices (Ayn, AyaNeo etc), but not all will be so powerfully, and beside that, native game will be more optimized and won't drain battery so hard as emulated one.
And beside SteamOS there are other Linux distributions, and not everyone want's to configure additional tools like Proton to play some particular game, so normal build option for them would be very welcome.