Generally, they don't care and are not actively keeping track, but there are systems in place that will throw a red flag if you're ordering the same model of computer 5 times in a year. The real purpose of the rule is to make sure you're not buying a bunch of Macs and selling them for a profit. (The terms of sale on almost any discounted Mac state you can't resell the computer for 1year after purchase, not sure how they track that though.)
I was a business specialist in a retail store and there was a system for tracking unusual purchasing habits by business customers that spent enough to earn discounts. Way back during the iPhone 3G launch Apple would also track a checksum based on credit card information to ensure people were not buying large quantities of phones to sell on the grey market. I can't remember the exact limit, but it was something pretty high like 15 phones per month.
For education discounts Apple retail will take the ID number off the gov issued ID matching the credit card/check you pay with and your student ID. I never had the system throw any errors or stop a transaction from entering the ID number, but I assume it is being tracked somewhere.
In all I wouldn't worry about it unless you are trying to do something shady like trying to resell. I had a family come in one day, 3 kids in college and mom and dad, all got new computers. 3 Laptops and 2 iMacs. Education discounts on all since students qualify for 1 laptop and 1 desktop. Had to be rung up in 3 transactions using dad's ID each time, no issues. I only wish I had been so lucky to have awesome parents like that...