Q: When asked to clarify a point to the reviewer, should I do so in the paper itself or the response to reviewer?

Thank you for your query! One of the great strengths of the peer review system is that reviewer comments allow you to present a more well-rounded, comprehensive, and compelling account of your work, so taking advantage of any points of improvement raised by the reviewer, by making the relevant change to the manuscript, ensures you also improve the presentation of your study to your readership. Moreover, especially when reviewers raise clarification points around methodology, they may be raising questions that other academic peers would also have when reading the same manuscript, so it is a good idea to make such changes to the manuscript as well as clarifying the point for the reviewer’s own benefit. On the whole, there are good reasons to make changes to the manuscript in accordance with reviewer comments and usually very minimal drawbacks to make those changes, so the general recommendation would be to revise the manuscript accordingly, though of course it is always best to examine the specific case under consideration before making this decision.