And the idea of building a separate horde base actually sounds nonsensical to me. This is already "meta gaming" - you can't protect your valuable stuff by securing a base so you build a "fake base" that has nothing valuable in it. That's not intuitive, it only makes sense in 7D2D.
Nonsense. Think of any location in The Walking Dead. Each family unit keeps their valuables in one place - a jail cell, a suburban house, a hotel room - but they don't fight the zombies from that location if they can help it. They get up in a guard tower, or patrol the outermost fence, or go further afield to find the zombies proactively. Whether it's part of the same base can become somewhat semantic, but when given the chance to design your own living arrangements, it's not "meta" to plan against fighting out of your bedroom, your workshop or whatever place is considered valuable.
And if, conceptually, verticality didn't proffer an unbalanced advantage in gameplay, strong and/or thick walls would still be just two of several options, alongside traps that slow, traps that damage, traps that redirect (mazes/funnels/pits), melee weapons, ranged weapons, and yes, stilt and underground bases. Players, as always, could use all of these in various degrees according to their preferences, except each of them would be brought into balance instead of some being infallible. Overwhelming a new/casual player wouldn't be balanced, and neither is a strategy that's
infinitely effective.
faatal's posts about zombie pathing have been particularly encouraging, and I think in A17 once we get over the residual fear of wandering hordes tearing through surface buildings for no good reason, we'll get comfortable putting stations and storage on the ground floor again.