I am not sure what your objection is. You are saying that most people don't do a good job? True but IMHO irrelevant. As the saying goes, there is no real difference between Perl scripting and Perl programming, but the ones who think of it as programming generally do a better job.

As you note, scripting the problem straight through makes it harder to understand later than programming it properly. As you mention, people often script and then try to solve their problems with volumes of documentation. At which point you have two problems instead of one.

Documentation is both good and necessary. It tells people what they can and cannot expect, it tells people what interfaces should be used and how to use them, it provides a spec by which the programmer figure out what the code should be doing, it provides something for testers to test and it helps users.

It does not replace the need to program well.