I don't know what you are asking when you ask whether the SA was "blowing smoke," but to address some of your specific points:
1. Walgreen's does not sell fakes. Your Creed is genuine if purchased from Walgreen's.
2. I have no doubt that a Creed SA in a Creed Boutique is probably trained in what differentiates genuine product from fakes.
3. I would expect a Creed rep to downplay batch variations.
4. Some here on basenotes don't believe there are significant variations, either, and I respect their noses. All I can say is this: the only two Creed fragrances I buy with regularity are GIT and MI. I absolutely know there can be (not "always are") distinct differences in these two scents from one batch to the other. And other basenoters I trust have the same opinion about other scents. I am not an alarmist, and have not experienced variability with any other fragrance house. It is simply something you have to put up with if you love Creed's scents.
5. I have no idea how many people "actually make" Creeds, nor do I know what this means. If the SA meant that there are only 35 people on the production floor combining ingredients or operating the production line, I would have no reason to disbelieve that. Creed isn't the size of Chanel, and I suppose (again, I don't know) it produces its scents in one single factory.
The Creed SA's get uniformly high marks here on basenotes, and I'd probably put a lot of stock in what they say. Just remember they work for Creed and therefore should be expected to downplay its blemishes.
Oh, and I am absolutely NOT a Creed expert! These are just my thoughts.