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 t

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.