I'm no modder (or even programmer really), but surely there's a way to cheese this even with existing mechanics.
Here are my way too optimistic ideas:
1. place two distinct bases right next to each other, that are linked somehow.
either you could have other levels placed automatically after you place and arrange the initial one, or have an "add level" button next to the "build new base button", for a cost that would be cheaper than making a whole new base.
these would be custom bases that are automatically named "[original base name] level 2", and have some way of sharing inventory and soldiers.
they would be shown as separate bases in the base selection menu, and maybe you could edit the list so that new levels were added next to old levels of the same base.
(I think it would make the most sense for new levels to be located further down (for base defense and imagination purposes))
2. sharing inventory could work by using the original base as the only inventory, then sensing when a new facility is added/removed to/from the level two/three bases, and add/subtract inventory space from the main base accordingly, while the level two/three bases don't have any increase in inventory ever.
alternatively if you couldn't sense when another base had something added, you could just set the transfer cost between the different levels to zero. this would be more annoying of course, but I think we could deal if it was the only way.
3. base defenses would be difficult of course. I imagine it working something like cydonia, where you clear one level first (starting from bottom?) then move up, with new levels generated by starting distinct but linked base defense missions on the "other bases" sequentially.
Sharing inventory would of course still be a problem here even if the above ideas worked.
it would be nice to be able to transfer soldiers and gear from the bottom levels to the top as you go, but if nothing else separate inventories could be used and you'd just have to have stock each level accordingly, then imagine that they're all happening semi-simultaneously to avoid immersion breaking.
so yeah, hope some of those work. I'm not feeling up to the task of actually learning the game well enough to try this, so... good luck.
--- posts merged to help both your OCD and mine - Solarius Scorch ---And of course each new level would need an access lift as an elevator, which is also where aliens would spawn for the multi-level defenses.
that's probably obvious, but my ocd requires complete communication.