Bob Turner posted this answer on another forum:
A year + ago, I had to call Williamsport (I wanted the larger starter motor, which they exchanged with mine for no charge). While I was on the phone I asked them the difference between "X" and "Y", since this appeared to be new at that time. He said there is no difference. Just that Lycoming decided they wanted to keep track of where engines are going, so experimental engines sold by Vans are "Y"'s; those sold by others are "X"'s. At least, that's what he told me. Presumably if there was another large retailer, those would be "Z"'s.