One polite response begins with your reasons, some revisions for clarity where you think the reviewer went wrong, and then "I have clarified..." - unless the reviewer is blatantly unqualified or grinding an axe, in which case, ugh, who knows, depends on the editor.
When I've submitted revisions to the editor, I explained in my cover letter that I clarified/corrected points a, b, and c, but that point d remained the same because (my explanation why the dufus was wrong). Will be interested in how your situation turns out. Both times this happened to me the editor went my way.
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