The Philosophers' Cocoon

In our newest "how can we help you?" thread, a grad student asks:

Suppose after submitting a manuscript for review, I get back comments (perhaps I even get the verdict 'minor revisions'). Am I allowed to make major changes to the manuscript beyond what the reviewers recommend, and should I note this somewhere?

Basically, while waiting for reviewer reports, I've gotten feedback for the paper from a conference and want to make some major changes.

Good question! Strictly speaking, you're "allowed" to do anything you want. Revise-and-resubmit verdicts are technically rejections where you are simply invited to resubmit the manuscript for another round of review. The more salient question is what the wise thing to do here is, and I think that probably depends a lot on your situation and what you value. Let me explain.

Obviously, it's your paper, so if you think there's some major issue with it that the referees didn't spot that would make you unhappy publishing it without the major changes, then perhaps the changes are worth making, whatever else happens with the R&R. But, and I think this is the key thing on the other side of things, making major changes that the referees didn't ask for might make the referees (and editors) unhappy and inclined to reject. Perhaps if you explain well why you made the major changes in your 'response to reviewers' document, it might work. But I don't think I've ever done anything like this, and it seems to me a really risky thing to do, especially if the OP is a grad student who needs publications to get a job. I messed up a few R&Rs at good journals while in grad school, and if I could go back in time and do things better, I absolutely would.

But these are just my thoughts. What are yours? It might be good to hear from people who have experience publishing, both senior and junior people, on what you do and think about cases like this!