Because Cari tells his stories the same way old-school Japanese eroge devs approach theirs: in that despite the choices there is only one true route and that said route has a bigger chance of being carried to the next game. And that's because it's much easier to write around it instead of taking into account multiple permutations that won't even matter in the long run because at the end of the day these are visual novels with set stories and not large-ass RPGs where decisions affect worldbuilding and major story events. It's for that same reason that AVNs with branching paths never get a sequel of sorts unless they choose a canon ending or simply carry over superficial consequences that ultimately wouldn't matter in the next game.
That said, Eternum will likely be the same: it will have multiple endings, sure. But there is likely only one true ending that will essentially shape the events and conditions for the next game (provided said game takes place in the same universe as this one and OIAL, anyway).