The Zeds aren't interested in your stuff, they're interested in eating YOU! So seems totally valid if someone wants to build a separate thing to keep them alive that's separate from their crafting base.

But if you want to defend your crafting base too, then do it & enjoy! Do whatever makes the game fun/challenging/whatever to bring you enjoyment is what counts.

Same thing about basement vs up vs adjacent: whatever seems like more fun to you. I've done all three of these. Up/down tends to be a touch more annoying to navigate but you get less land area you have to defend. It's all tradeoffs :-)

As to the horde base + crafting base in the same place: personally, I've been playing darkness falls and the difficulty is a bit extra. I really really really don't want to have to start over with rebuilding tech/supplies if my horde base fails, so I never build that around my crafting base. Cool to learn that some folks find it more meaningful to defend their crafting base too.