Actually, yes, he did mention packaging headaches as well. MATLAB manages to sidestep the issue by not having a package manager, and basically forcing you to include the literal source code of any non-mathworks dependencies in your repo.

We do need a better story with dependencies in Python, and I'm happy to see there have been several posts over the last week talking about this issue.

That said I think that for academic projects it can be fairly straightforward to handle after an initial learning curve. A lot of projects can be accomplished with just numpy/scipy/matplotlib and maybe a couple other specialty libraries.