My experience with PDL is that it is a great way to produce code, but not to maintain it. Also I find in Perl that it works better to, instead of turning the pseudo-code into comments, turn it into function names. or Perl.

I agree with you that things are changed somewhat because Perl is already a high level language, so the gap between what you are trying to do and how you do it is narrower than it might otherwise be.

Should you wish to go the other way and make PDL into comments, you will wind up with densely commented code. While you had a good experience with updating it (largely because you chose to also update the comments) it doesn't age so well. This time around you likely left some comment in there which does not quite match the code. Or if someone else edits it they will. Add a few rounds of that and the comments will inevitably drift out of sync...