True, but the students that re-implement these codebases also might have a much greater understanding of the underlying techniques, theory, and the interaction

True, but the students that re-implement these codebases also might have a much greater understanding of the underlying techniques, theory, and the interaction between them; compared to others who produce more results, but use these codebases as black boxes. I think both pathways lead to equally good academic careers, they just branch out into separate paths.