The whole point of the things is to give an impact and dimension to the place. If you don't have the proper scale, you don't have the proper impact.
Had I been consulted about the size of the pools, I'd have advised the architect to have them match the footprints exactly. However, even with the way they were built in reality, the tree line does provide a concrete outline for the kind of impact you want. The idea is that when you walk through the tree line (the original façade), you're inside the tower. If I had a say in the matter, I would erect replicas of the façades to replace those trees to demarcate the memorial even more starkly.