I'd disagree on this. Is it important for the university to cover the theory (algorithms, compiler design/automata/languages/parsing, logic, discrete mathematics etc)? Absolutely.

Does that mean there isn't space for a module on software engineering theory (design patterns, development methodologies, OOP principles, testing, version control...)? I really don't see why that has to be the case. Some of the worst code I've seen has been written by academics - undocumented, undescriptive nonstandard single letter variable names everywhere, huge monolithic functions named "compute" that span hundreds of lines and several levels of indentation.