I don't know that our definitions are that different. Most of the over-engineering I've seen in practice was done in the name of simplifying a complex problem, but resulted in a system that was too rigid to adapt. Our definition of "over-engineered" might be different, though.
As someone who's worked for a large part of my career as a sort of bridge between academia and industry (working with researchers to implement algorithms in production), both you and the original author are right to an extent.
On one hand, academics I've worked with absolutely undervalue good software engineering practices and the value of experience. They tend to come at professional code from the perspective of "I'm smart, and this abstraction confuses me, so the abstraction must be bad", when really there's good reason to it. Meanwhile they look at their thousands of lines of unstructured code, and the individual bits make sense so it seems good, but it's completely untestable and unmaintainable.
On the other side, a lot of the smartest software engineers I've known have a terrible tendency to over-engineer things. Coming up with clever designs is a fun engineering problem, but then you end up with a system that's too difficult to debug when something goes wrong, and that abstracts the wrong things when the requirements slightly change. And when it comes to scientific software, they want to abstract away mathematical details that don't come as easily to them, but then find that they can't rely on their abstractions in practice because the implementation is buried under so many levels of abstraction that they can't streamline the algorithm implementation to an acceptable performance standard.
If you really want to learn about how to properly marry good software engineering practice with performant numerical routines, I've found the 3D gaming industry to be the most inspirational, though I'd never want to work in it myself. They do some really incredible stuff with millions of lines of code, but I can imagine a lot of my former academia colleagues scoffing at the idea that a bunch of gaming nerds could do something better than they can.