Maybe they forgot to run disk utility 🙂
As to why, who knows? Keep in mind that Apple's customer support is all about keeping you happy, so if you say the hard drive is too noisy it's not going to be hard to verify because, well, they do make noise.
But just because they replaced your machine doesn't mean that the replacement will be any different with respect to the hard drive. Sometimes, info from the mothership, such as the technote above, doesn't matriculate to the Apple store employees in a resounding fashion. For the most part, Apple store folks seem to default to when a customer comes in and complains about something, and they can verify what the customer is complaining about, they will replace the product without any further evaluation.
Keep in mind that everyone's environment (ambient noise, room size, etc.,) where they use their machines is going to be different, so hard drive noise isn't going to be a universal problem as probably a lot of folks won't notice or if they do, not loud enough to be a concern.