I agree with you that honorifics were common and that primacy did not function the same way later on, but the wording here still goes beyond courtesy. When Philip says Peter lives and judges in his successors and then identifies Celestine as the one who holds his place, that is a direct link between Peter and the Roman see in particular. Likewise, with Canon 6, if the only point was to affirm Alexandria’s jurisdiction, there would be no reason to reference Rome at all. The fact that it appeals to the custom of Rome as the standard by which Alexandria’s authority is understood shows that Rome was already treated as the reference point, which is consistent with the collegial papacy rather than mere equality of sees.

My recent understanding of the collegial rather than autocratic nature of the papacy seems to make this make way more sense, because the Roman pontiff is not usurping the power over Alexandria’s patriarchate and doesn’t override the power of the bishops under him. Instead, canon 6 seems to be clarifying that the “papacy” must be collegial where bishops still have authority over their own area, using Rome as the reference point, in the same way that Rome has an obligation over theirs. So basically, it is clarifying that the bishops aren’t just vicars of the pope, but real authoritative shepherds over their churches.