Both sides of this argument are correct because both sets of practices are used for different purposes. A mid-sized or large software project (say 100k+ LOC) w

Both sides of this argument are correct because both sets of practices are used for different purposes. A mid-sized or large software project (say 100k+ LOC) with single letter variables all over, global variables, etc. would be an absolute maintenance nightmare. So the software engineering perspective is correct there. And in large projects it really is helpful to split projects up into multiple directories, use higher level abstractions, etc. At the same time, most scientific code bases are not in that category. They don't have dozens (or hundreds) of people working on them, they're not going to be expanded much beyond their original use case, and they're mostly used by the people writing the code and/or a small group around those people.