Apple, for whatever dumb reason, has _never_ enabled Trim on non-Apple branded SSDs.
I don't work for Apple, but... Older MacBook Pros came with instructions for replacing the RAM and hard drive. This was considered a normal thing to do and didn't void warranties. For example, my 2011 MBP has normal Phillips screws on the bottom, and it takes me about two minutes to have the back panel off and the RAM and HDD snap right out.
SSDs have a history of notoriously horrible firmware. SandForce, anyone? Someone goes to Best Buy and comes home with a new SSD, pops it into their MBP, uses it for a month, and the thing asplodes and eats their data. They call Apple support to scream at them for writing a terrible OS that loses their data, and Apple loses money and reputation.
I can imagine perfectly non-nefarious reasons why Apple would disable TRIM by default and only enable it for drives that have been explicitly tested for compatibility. Even today, you can still turn TRIM on for yourself as you described, at the price of reverting to pre-Yosemite security. I haven't done so on the 840 EVO I swapped into my MBP because I've judged that it's not worth the tradeoff for me, but it's an option. Trim Enabler even has a GUI to do it for you.
I'd be hard pressed to come up with more of a manufactured controversy.