The chart/formulas for all the monster numbers by level are a guide. They are not rules, in the sense that a 19th level monster must have an AC from 31 to 34. They're a starting point.
Some DMs will just crank the numbers out and be happy without delving into the system math. The system works fine for these guys.
Others will want to account for all the numbers. For NPCs, we've included a "skill" rating of sorts, an abstraction of feats and magic items that allows you to give NPCs vanilla gear without messing up the numbers or giving the PCs tons of magical weapons and armor in addition to their normal treasure.
For monsters, things might be a little trickier if you want to account for all the numbers. You might give your level 18 demon a suit of plate and find that his AC is a little lower or higher than you want. In that case, you can either accept some wiggle room and change the number or find some reasonable explanation (the guy wears plate, but his AC is a little higher than expected because he has thick skin; you give him a shield or a couple of feats) or tinker with his attributes.
Running the numbers in my head, I think that using vanilla equipment as a base leads to reasonable, expected results. However, the need for an extra factor increases as you gain levels, particular for extreme case monsters.
In any case, you can still simply create NPCs. The abstracted "NPC skill bonus" is designed to allow them to use normal equipment and end up with reasonable numbers. We want to avoid a game where the PCs cart around huge piles of +1 and +2 armor and weapons looted from their foes. It messes up the standard rate of treasure and can lead to some absurd game world questions.
Damage is a little trickier. If you create a 12th level monster and give him a club, his base 1d6 damage isn't much for a 12th level guy, and if you boost his Strength you might end up with an absurd number.
In designing monsters, we accepted that the monster's attack is more than a sum of its weapon die and its stats. It also represents the monster's combat tactics and tendencies.
For instance, an ogre might do more damage and have lower accuracy than you expect based on his level, Strength score, and weapon. This reflects the ogre's wild but powerful swings. We essentially built Power Attack into his stats.
The really, really important thing with the system math is that it is all a guide. As a DM, it's up to you to decide how and why you want to tinker with stuff. The key lies in paying attention to the expected numbers, looking at your creature in light of those, and thinking of tweaks you can make to create a balanced package. Maybe you design an ogre gatecrasher who does a bit more damage than normal for his level, but you drop his AC or attack bonus a couple points to compensate.
As an example, I designed a monster for my home game that deals double normal damage but has half the normal hit points. It leads to a really swingy fight, but that's my intent. I want the PCs to be scared of a high damage roll from the guy, and eager to use their big attacks against him to knock him out quick.
Ideally, DMs will see the guidelines that they can use, abuse, and bend all they want to create the effects they are after. The thing that makes me happy about this system is that it "telescopes" to fit the DM's needs. You can spend as much or as little time building these guys as you want. If you need something quick, you can pull out the baseline numbers and use those. If you want to spend a while sculpting an NPC or monster to do something weird and interesting, you can dive into the system and do that.
I hope that the system provides a nice middle ground between a rigid mechanism and hand waving. There are rigid mechanisms in place, in that we crunched the math, created baselines, and built rules to get you to those baselines. However, those mechanisms are built to serve the end result. If you know that a level 8 monster should do 12 damage per hit on average, the game doesn't care whether you get that 12 via an arbitrary 2d8+3, or if you decide to give the guy a greatsword and a 20 Strength to make his damage 2d6+5. If you choose to make the guy's damage above average for his level, you know ahead of time that the guy hits harder than expected and can either design around that or just tell the players to suck it up.
The game basically says, "You're the DM. You decide, based on your campaign and your personal tastes, how you want to achieve these ends. It isn't our place to dictate that sort of thing to you."
