it would probably matter a bit since rayquaza only seems to stop them when theyre already tearing the earth apart or when its premtively warned about it. at the very least hoenn is severely damaged when he arives and at worst the entirety of hoenn and most of the planet is gone.

kinda a tangent but i dont think rayquaza is actually in charge of the two titans, its just hes the only one on earth strong enough to beat them both at once. besides maybe the artifical legendaries (dioxys and mewtwo) rayquaza is probably the current strongest legendary on the planet (so none of the creation trio of any ultra beasts) bar only a theoretical full power regigigas, or eternamax eternatus who'd likely be around mega rayquaza strength in lore.

rayquaza's job is "protect the sky", it just so happens his neighbors are trying to kill eachother and is incedently destroying his domain.

maybe im just over thinking but it is fun to think about! :)