“For example, still-soft, flexible material was recovered after demineralization of well-preserved bones from the Late Cretaceous dinosaur Tyrannosaurus13, whereas proteinaceous material was found to be preserved in another dinosaur, Brachylophosaurus14”
Note that the sample was demineralized. In short, and as the article repeatedly says, these are fossils and the time scale is geologic. It’s not proof of 4,000 year old dinosaurs. The lattice of the mineral fossilization preserved the soft tissue within and, in no way disproves the age of the fossil.