As a former Mac Genius and AppleCare support engineer, I'm very familiar with this policy. Apple pays a premium to ensure they they get the best displays being produced by their suppliers. However there is still no cost effective way to produce perfect LCDs every time. As far as I know these quality thresholds are actually enforced by the LCD manufactures. If the display falls outside of the acceptable range then the display can be returned to the manufacturer at little or no cost to Apple.
The displays being produced fall within priced tiers of acceptable pixel anomalies. For example, Apple may be paying a manufacturer for displays at a certain size guaranteed to have 8 or less pixel anomalies, while Dell could be paying the same manufacturer much less for displays that allow for even more. In the end it means Apple displays will cost more and will generally be of higher quality and have fewer pixel related issues, but they can't guarantee that all LCDs will be free of problems. Of course they would love to provide perfect displays every time, but I was told the cost of doing so would force the computers to be up to 3 times more expensive. Unfortunately it's just a current limitation in the process of producing the panels.
Of course, like others have stated these are mere guidelines and there is always room for some flexibility. Generally every complaint would be considered on a case by case basis. The position of the pixels on the screen, their color and their proximity to each other are all factors. However, when Apple replaces a display or machine that falls within the acceptable range, they eat the costs. And although rare, I had personally overseen cases where the replacement machine had more pixel anomalies than the original. This results in not only an unnecessary cost to Apple, but in a customer who is even more unhappy than beforea real no win situation.
Even Apple employees aren't immune as I've had the problem myself. I wasn't exactly thrilled about it either but I at least tried to see the issue from their perspective. In Apple's eyes these machines are not defective or damaged. They have passed all the QA tests are well within what is considered normal. I don't really think they're trying to fool anyone.
Besides if one wants a prefect display, they just have to be willing to pay for it. Apple will allow anyone to pay for a replacement display as many times as they want until they're happy with it. It's not worth it to me, but there have been some who paid more than once to do just that.
And yes, courtesy, patience and kindness towards the support staff will go a long way. Most of the employees genuinely enjoy being able to help a customer and they are much more likely to fight on your behalf if you're nice to them. Belligerent people with bad tempers will more often than not encourage them to follow the guidelines verbatim.