In SFIV some moves have throw, strike, or fireball invul, so TT always beats throws, and EX TT always beats hits (assuming the throw or hit does not also have throw invul), Also, ground to ground throws always beat normal attacks if they would otherwise trade, and I think air to air throws are the same, although ground to air throws (like soul throw) will however “trade”, so there’s more going on than just hitboxes.
In 3s (and SSFIV AFAIK) you can punch kunai’s out of the air. I think you can do the same to rocks in a3, although I could be wrong. This could be explained by hitboxes, if you assume the kunai and rock have their own green hitboxes, and one hitpoint of their own. This might not be how it’s programmed however.
In general, however, it’s a work thrown around by people who do understand the system (pretty much everyone who posts a decent amount on SRK is going to understand hitboxes), but realize that fussing over details isn’t important. In general, priority is discussed in a particular context, as in, this move has a good hitbox for this purpose. Lots of people will say Rog’s cr fierce has good priority, but you wont see them attempt to use it as a poke or counterpoke, because it’s understood that this is shorthand for “it’s hitbox and speed means it will beat out most jump in attacks”, and since every idiot knows that there’s no such thing as actual priority, then that’s the only possible meaning.