While Travis is running down the road in the intro credits, you're already passing through the smoke. But when Travis arrives at the house, he then identifies it as smoke. He would've known it was smoke just after he'd just gotten out of his truck.
The smoke was probably thinner where he was running, and knowing Silent Hill it was mixed with SOME fog. And who knows, maybe the game designers just forgot to program in a working nose.
I've always thought that it was fog that Travis was running through. As you see in the beginning clip, it's raining. After rain there's most likely fog. And Silent Hill (especially in Origins) is a foggy little town.
BUT then he does kind of say "It's smoke" like that's what he's been running through the whole time.
I reread your question and I don't really know how to answer this. I'm guessing it's an observation so it's a very interesting one.
Even if he WAS running through fog, have you ever been within half a mile of a bonfire? You KNOW something's been burned because of the smell, regardless of the presence of smoke. Likewise, he SHOULD be able to smell a burning building, and even see orange highlights in the fog since it's dark out.
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Its kinda a given that he smelled the smoke from the fire through the fog.
Like im sure he smelled the meats in the butchery, but he doesnt always comment on his experiences.