I really dont see what the problem is here. At the moment the game is designed with no proper threats to underground bases. In my opinion that is not a problem. My crafting stations are often underground and i still fight every hordenight in my arena and go out looting almost every day. Just as in real life, i tend to spend my nights indoors (and if one compares this to RL, one sleeps at night, so very safe location is needed), only in the game i dont need to sleep, so i build, i dig, i craft, and during day i go out hunting, farming, killing, building my arena.
And in the end, alot of people enjoy building to see what they can build in survival where you have to gather and mine all the stuff you need to build, and i am one of them. There are options one can change to make it harder to go underground, one can change what you can build and use, so if the vanilla game is not good enough, go and change it. Just like some other games, factorio for example in my case at the moment. I got bored with vanilla so started using mods.
The same applys here as well, the devs have a goal in mind what the game should look like when done. If they say no zombies underground, that is not an exploit, if they say there should be, fine as well, i will adapt or find a mod that takes them out of underground if it can be moded and i dont like it. But they are giving us moding options so we can make the game more to our liking.
So back to beginning, i really dont see a problem here.