Right, but the article seems to imply that all code should be in a single file.

It seems the author indeed is not a SW Engineer and thus does not really grok the benefit of "modules".

This of course depends on the size of the program. Small program "fits" into a single module.

And I think that scientific programs are basically small and simple because they don't typically need to deal with user-interaction at all, they just need to calculate a result.

Further I think scientific programs rely heavily on existing libraries, and writing a program that relies heavily on calls to external libraries produces simple, short programs.

Scientists produce science, engineers produce code-libraries.