The stats for the creatures includes their ATs BUT what if a hill troll happened to have full plate on (AT20)? Would you use the amour's AT and ignore the fact that the troll has it's own naturally tough skin (being AT11 as it happens) or would you somehow combine any results for the attacks between the ATs?
AT20 would be the AT used, and the natural would be ignored.
Unless, you are using the new AT rules from Combat Companion, in which case, any natural AT adds to the DB, and thus can/does stack with armor worn over it.
(on a side note, there's loads of codes that need deciphering before you can drop them into the encounters like is speed and initiative bonus - why couldn't they have just been listed?)
(on ANOTHER side note - I used a 'Lesser' Great Spider (stats on page 54) and it has a '40 OB in Small Sting' with the double arrow after after it which means that if it got a non-tiny critical with that attack, the next attack applies as well. In this situation, the next attack was poison. Unfortunately, ALL criticals on the Small Sting table are 'Tiny' no matter what AT their against! So why have that in the stats if it's unachievable - unless I'm interperating the rules wrong?)
Did you read the notes on the Stinger attack table? The first note saying that any result with a critical injects a poison?
The codes and such are a general guideline, plain and simple. Notes on the actual attack tables will over-rule the notations (i.e. stingers will do poison attacks, regardless of the critical type, if a critical is done).
The use of the symbol for the spider is meant to indicate that the second is usable ONLY if the first succeeds.
For other creatures, there WILL be cases where the secondary attack is not a poison (and the primary attack is not a stinger), and therefore, the non-Tiny critical note will apply.
The codes for things like MA/AQ are done in that manner because they can be applied to multiple things and give different bonuses based on what they are applied to.
Also, remember, the folks who originally made these rules are no longer around, so there is way we can be sure what their reasons for anything might have been.