>>57898695 (OP)Wormholes don't appear in space, or at the level of the ozone layer, so it's a bit beyond Rayquaza's jurisdiction. He prefers to deal with Groudon and Kyogre and external threats such as meteorites.
On the other hand, Zygarde was on hand to deal with the Ultra Beast threat, because it threatened ecosystems, and therefore the world internally. As for Eternatus, a pretext for creating a story, Rayquaza should have taken care of it.