Including a note to reviewers in a submission I submitted an article to a journal, and it was rejected. The reviewers criticised some configuration values I used in my software. The comments were very helpful.

I have since improved the software, re-run the experiments, and extensively rewritten the article. I plan to submit it to the same journal. I suspect there's a good chance it will go to some of the same reviewers. 

The controversial configuration parameters are no longer needed, and so are not mentioned in the article. I'm worried that if the reviewers saw the earlier version of the article, they may be confused by the "missing" parameters. 

For this reason, I am tempted to include a note explaining the change. Is this a reasonable thing to do, or would it seem amateurish? Would it be better to just communicate this to the editor instead of including a note in the submission itself?
When resubmitting a paper after rejection, many journals require the authors to provide a detailed response to reviewers, whether or not the paper is going to be assessed by the same reviewers.

Therefore, instead of including a note to explain the change, include a complete response to reviewers, even though the journal you are submitting to does not require it. It would be useful even if the reviewers are not the same, because it's quite likely that new reviewers will receive the initial comments.