I believe the ongoing theory for Justicar skins is that they follow a different timeline than the current one where Syndra and Atrox are not aligned with darker forces.
Arc'Light: I have theories for the other two outside of Varus's. Vaynes could be a prediction of her possible ascension (as it seems just about anyone can ascend so long as they get the favor of the gods/are really good at what they do; Janna's old(did they change hers yet?) lore comes to mind). Whereas Vel'Koz would be more of another alternative line type thing or even an evolution/change of his current form.
Other than that most of the skins are about alternate timelines like Creator Viktor as he wages war against Runetera, thus creating the Pulsefire or Fullmetal line. I'm not really sure which of the two it was.