Steelhead and salmon, once they return to freshwater rarely eat, so they don't often swallow bait. If this weren't the case, there would be a lot of deep hooked fish while bait fishing. They do, however, pick stuff up out of instinct and if its edible, its more likely to be worked on for longer periods before spitting it out and so the chances of hooking one deep is greater. I've watched fish in the Rieter hatchery creek do this. Drop in some eggs and they pick it up, chew on it, you even see egg goo coming out of the gills, then they spit it out.

Non-bait (corkies/yarn etc.) is usually spit out fairly quickly, because its completely foreign.

I've hooked very few fish deep with bait. I think its a function of when you set the hook; just don't let him jaw on it for a few seconds. I've heard of more fish hooked deep when free drifting. When fishing this way, I think the fish can inhale the bait without any resistance so your more likely to get him in the throat or gills. With bait divers I think kind of the same; your backing the fish down with a large bait with 2 hooks, and he inhales it aggressively. I've hooked fish deep on pink worms because the fish inhales the whole thing while the hook is in the back 3/4s of the worm.

Set the hook as soon as you feel'em, and your less likely to deep hook'em.