@gello22: Looks awesome! The more I research how tree roots grow, I think you're right. Trees don't poke holes in liners. They find holes that already exist and exploit them—like the seam between your skimmer and liner or an imperfect weld in a seamed liner. They may also send surface roots that will go over the liner and, as they increase diameter, will push the liner down causing a low edge. Or maybe as they increase diameter along the edge of a liner, stretch it beyond its bursting point.
But the idea that a tree will say, "Look, a pond! Let's poke a hole!" seems almost impossible. I think people find tree roots in a hole in their liner and assume the tree put it there when it was already there and the tree just moved in after finding the moisture outside the liner.