Not getting involved the whole legal conspiracy theories, looking at the second part of your post, I do see some problems with that. This one method is already convoluted enough. While many of us understood how it worked, it still had to be explained to others. I'm not trying to insult intelligence but sometimes things just don't click with everybody. We all process things differently, and like I said, this code, while very nice, is already convoluted enough as it stands.
If you start introducing simultaneous stat edits using items (which would probably have to be standardized like the master ball is), it would create all sorts of havoc. Could you imagine Datel's inbox? I would imagine that they want to keep it as simple as possible.
To be clear: only one of these would be active at a time. Sure, this would be a roundabout way to do things, but it's the only feasible option at the moment for any but the most basic edits.
I don't see how this would be so much more convoluted. The move index might be, but that's just a list.