Based on the information in the Guide for Language Settings>Alphabetic characters, it seems that they do want you to put the glottal stop in the Alphabetic Characters list, on its own line. Then Paratext will no longer divide words which contain glottal stops.
A similar thing can be achieved by putting things in the Other Characters> Word medial punctuation. But I think in the case of the glottal stop, it is correct to have it only in the Alphabetic Characters field.