Data independence doesn't (yet) exist. We can decry that fact, or we can live with it. We certainly shouldn't encourage it.
Standardization at the physical level does ( sort of) exist. Vendors hide this by using different terminology for everything, but the fact remains: there are pages and extents and read groups and files and partitions and tablespaces. There is, in fact, a Storage Hierarchy.
Migration is a serious problem. Fragmentation is too, but takes a long time to show itself.
Normalization is a good thing. No good thing is all good.