How can paleontologists identify morphologically different fossils as members of the same species?
Radically different body shapes and sizes represent overall phenotype. Overall phenotype was used briefly in the 1960s and 1970s for species identification under a statistical distance method called "phenetics". However, phenetics has been rejected as a valid method of species identification. Similarly, although ecologists widely use the Biological Species Concept (Mayr) based on reproduction, taxonomists generally prefer some form of the Phylogenetic Species Concept. In addition, paleontologists find species concepts that require assumptions about reproduction in fossils to be difficult. The phylogenetic species concept uses the presence of fixed morphological characters to identify individuals as members of a species. Fixed characters need not be major, obvious differences. They need only be present in all members of a hypothesized species, and absent outside the species. That they are fixed in all members of a species implies a lack of gene flow, but the definition does not require that. So in the example you gave, juvenile T-rex must have some unique characteristic morphological feature that define them as members of the species (a synapomorphy). In addition, when there are a series of intermediate juvenile fossils, it becomes possible to link them together.