Bear with me here, I've yet to really delve into SR4 and I feel like I must be missing something as I'm throwing a character together.

The Control Rig Booster (a nanoware system) specifically states that it requires a Control Rig cyberware implant , then says that it provides bonus dice (but clearly reminds you that it is capped by the augmented skill maximum).

Under what, if any, circumstances is this puppy worth it? Say you've already got a specialization in the skill in question (+2 dice), and you're required to already have the Control Rig implanted (for another +2 dice)...doesn't that mean that under no circumstances will this piece of nanite goodness ever help you out, since you're already at/above the maximum boosted dice pool (even with a 6 or, with Aptitude, 7 for your base skill)? So is this nanoware system only good if you aren't specialized, and even then isn't it really only worth it at rating 1 (or 2, if you've got Aptitude and a maxed out skill)? And isn't this even leaving the possibility of someone being an Adept and scoring extra dice that way out of the equation entirely, along with stuff like Reflex Recorders and Enhanced Articulation and whatever else might be out there?

Or am I misunderstanding/misreading something about augmented skill maximums, bonus dice from specializations and 'ware, or both of the above?

Bonus dice for a skill test are not the same as bonus skill. The latter is limited by an augmented skill maximum, but the former is not.
So neither specialisations nor the control rig count against your augmented maximum, as they don't actually modify the skill, they just give you bonus dice whenever you use the skill.

No, it doesn't:

Problem solved.

So "a bonus" isn't the same as "bonus dice."

I don't suppose there happens to be a comprehensive list somewhere of the difference between the two, or of which ones count towards the augmented skill maximum and which don't?

Everything that only says bonus dice is infinite.
Everything that gives bonus without dice to a skill or attribute is limited.
Including such things like Bone Lacing it seems.