Glad to see I wasn't the only one thinking this. It doesn't matter as much now since we know that you need a Mewtwonite X/Y, but it would still be nice to know if you're able to stack them.
The reason why people believe X and Y refer to chromosomes is because on the Japanese boxart, you can see a DNA double helix below the title, which is the same DNA structure you see after a pokemon megaevolves.