The Kaf HaHaim says, however, that even if the person who came late is the one who is best suited to recite the repetition, he may not do so as there is Kabbalistic significance to praying the silent Amida before the repetition. The Ben Ish Hai (Rav Pe’alim, Sod Yesharim, vol. 3, § 7:2) disagrees and says that if such a person is the only one who can properly lead the prayer or has a Yahrtzeit, etc., it is permissible even Kabbalistically for him to lead recite the repetition in lieu of his silent Amida. Although ideally someone who comes late should first pray silently, when necessary the Moroccan custom seems to follow the Ben Ish Hai’s opinion to permit the person to recite the repetition only.
Summary: When necessary, someone who has a pressing reason to lead the prayer but came late may recite the repetition of the Amida, and does not have to recite the silent Amida first.