I think you are half right. Because I thought for the longest time that the Root and Claw fossils weren't in the game, because it took me a long long time to get them, but I did get both on my Y game. They proabably just have a much lower chance to get them, but you CAN get them on Y.
EDIT: Thinking about it further, my memory on the fossils was a little fuzzy, so I checked and it seems I got my Anorith and Lileep from someone else, so I was mistaken. My apologies Archimand.