Oh there's < 5% chance (lower honestly) that they'll add more than two layers. Pipes and belts have two layers (underground in their case). I think there's a graph theory theorem that you technically only need unconflicting crossings (~two layers) to be able to draw any valid network (that doesn't mean it'll be pretty but it'll be
possible, i.e. it can embed designs that the previous system would simply be unable to represent). Anyway, at this point having exactly two layers is a factorio theme.
I think you can rest easy if you're worried that factorio might implement more than 2 layers. I like the sound of a mission-oriented problem solving core loop. Maybe allow players to create and share their own missions, that could add an engaging social element. Good luck!