Maybe Apple gets too many Support calls from crappy 3rd party RAM and this is the only way to prevent problems that are associated with crappy 3rd party RAM. I know that buying 3rd party RAM is a crap shoot because there is a strong likelihood that the memory will become flaky after about 1 year and I know, for a fact, that there was a lot of problems with earlier 3rd party RAM not being compatible. Crucial had a lot of problems in the past with their MacMini memory and they would ship incompatible memory to people and it would take them a while to get their act together, but MOST consumers would call Apple Tech Support when they have any problems and then Apple's Tech Support has to help the customer troubleshoot the problem and instruct the customer to re-install Apple memory, and 99% of the time, that fixes the problem.
How do I know? I've had that problem myself, I've had friends with that problem and I've worked for Apple Corporate resellers (some of the largest) since the mid-80's and 3rd party RAM problems was a common issue. Apple just uses more reliable memory and it's tested to pass VERY stringent test, whereas a lot of 3rd party memory is hit or miss and much of it is what Apple discards, so you might be buying the crap that Apple wouldn't stick their name on. This has and will always be an issue with computers. I know it costs more, but there are reasons why.
In the component world, chip dumping is common, they usually start dumping chips sometime right after they release a new spec RAM chip.
If you have ever bought RAM before, it's common to see a different number of chips on the module even though they are the same amount of RAM. Apple has been getting (most of the time) RAM module where there are less chips on each module than what other 3rd party companies ship. Why would Apple spec out a RAM module with less chips? Simple, they don't require as much power to drive them. Crucial, at one point, was shipping RAM modules for laptops where they actually stacked the chips on top and then soldered to the RAM board. These were really bad RAM modules that had nothing but problems when installed. Either they didn't work or they became flaky shortly after they were installed. The reason was that they sucked up a lot of power, became hotter and thus had more failure. Crucial was selling tons of these things to people with Apple Powerbooks as they were cheaper, but having more problems doesn't make them cheaper in the long run because of the user's downtime and amount of time it takes to get them replaced doesn't work out to be cheaper, it works out to be more of an expensive hassle.
I always recommend using Apple RAM, pay the extra amount and get AppleCare and you'll be happier more often. Troubleshooting any problem is easier and you'll probably have less RAM related issues.