I sometimes give a talk to startup companies, in which I tell them why their code should be horrible. It's an intentionally provocative thing to say, but there is reasoning behind it, and some of the same reasoning applies to a lot of scientific code. The linked article has a few comments that tangentially touch on my reasoning, but none that really spell it out. So here goes...

Software development is about building software. Software engineering is about building software with respect to cost. Different solutions can be more or less expensive, and it's the engineer's job to figure out which solution is the least expensive for the given situation. The situation includes many things: available materials and tools, available personnel and deadlines, the nature and details of the problem, etc. But the situation also includes the anticipated duration of the solution. In other words, how long will this particular solution be solving this particular problem? This is called the "expected service lifetime".

Generally speaking, with relatively long expected service lifetimes for software, best practices are more important, because the expected number of times a given segment of code will be modified increases. Putting effort into maintainability has a positive ROI. On the other hand, with relatively short expected service lifetimes for software, functionality trumps best practices, because existing code will be revisited less frequently.

Think of the extremes. Consider a program that will be run only once before being discarded. Would we care more that it has no violations, or would we care more that it has no defects? (Hint: defects.) That concern flips at some point for long-lived software projects. Each bug becomes less of a priority; yes, each one has a cost (weighted by frequency and effect), but a code segment with poor maintainability is more costly over the long term, since that code is responsible for the cumulative costs due to all potential bugs (weighted by probability) that will be introduced over the lifetime of the project due to that poor code.

So, short expected service lifetimes for software, prioritize correct behavior over maintainability; long expected service lifetimes for software, prioritize maintainability over correct behavior. The source code written by a brand-new company will be around for six months (maybe) before it gets factored away, or torn out and rewritten. During that time, less-experienced coders will be getting to know new technologies with foreign best practices, and those best practices will be violated frequently but unknowingly. Attempting to learn and retroactively apply best practices for code that will likely last a short period of time is simply more expensive (on average) than just making things work. The same applies to scientific code, which gets run for a graduate degree or two before being discarded. If the code wasn't horrible, I'd think that effort was being expended in the wrong places.

In my experience, most "fights" about best practices (whether a technique should be considered a best practice, or whether a best practice should be applied) usually boil down to people who have different expected service lifetimes in mind. (One of those people is probably considering an expected service lifetime of infinity.)