Honestly, the performance of the raid is a huge part of this.
In a more Heroic-oriented guild, there are going to be a ton of on-pace-for-parse runs that will melt down due to mechanics failure. Not to mention kill times. They will be slower, which means parses will be lower.
When I went from my last guild to my current guild, all my parses went from blues and purples to purples and oranges. I didn't suddenly become a better player, it's just that my crazy proc openers led to kills more often, and those kills happened in a shorter amount of time.
I get what you're saying about people just not knowing optimal rotations, but by and large, I'd offer that there are a lot of people who don't know that they'd be putting out bigger parses if they ran with a higher-level guild.