Comments like "can you provide more information?" or "clarify what you mean" can become obsolete when the post gets edited. Should the comment be removed after the edit, or not? I think that removing the unneeded comments (those that do not contribute towards solving the issue) is the right thing to do, since it cleans up the question.
Yes. This is one of the primary reasons to flag comments for deletion. It even has its own reason in the comment flag dialog:
See also the section on When should comments be deleted? from the FAQ.
Comments are temporary "Post-It" notes left on a question or answer. You should not expect them to be around forever: Once a clarification has been made, an edit added to the post to include new information, or the issue in the comment is otherwise resolved, it is subject to deletion. In reality, many obsolete or chatty comments remain untouched due to the high volume of comments posted, but this does not mean that they can't or shouldn't be deleted in the future.