I have seen both "(Something) requires that one specify how.." and "(Something) requires that one specifies how.." used in various contexts. Which is grammatically correct? My sense is that the former is correct because the verb "specify" should be conjugated in present subjunctive within a declarative content clause.
Your sense is correct, but as I see you've determined, this answer correctly indicates that both are used, and both are acceptable (even if some of us think the subjunctive is more natural, and would never say otherwise).
Long live the subjunctive!
I believe that these can both be correct, depending on the specific tense and context. See this website for a chart: http://www.verb2verbe.com/conjugation/english-verb/specify.aspx