Bases are not safe until You Make Them Safe. There is really only one failsafe way to do this atm and that is only for non-flying enemies. You figure out a perimeter that seems sufficient. I use the running mode. I count running steps and when it hits 55 to 60 - that is one side, then same in other direction, squarish. Get out your trusty pickaxe and dig down about 3x height of your agile Viking.
(Where you place your base is up to you but for me it's somewhere in the meadows close to water, fairly close to Dark Forest and maybe mountain nearby. Up till this time I just have a shack near spawn.)
Dig yourself a lovely deep trench all around. Then take all that rock you got and stand at the inner edge of the trench and make a wall. Flattening the area is good, at least enough to put down a building or two, can terrace your gardens as needed. None of those silly block walls. They just get damaged by Mr Troll. The devs have made earthen wall building quite easy and very accurate once you figure out how it works. First one or two will be a bit fugly but who cares. Plan your gardens near the walls. Plants don't take damage from troll attacks, but buildings do.
I used to make lovely entryways but don't bother any more, they just get battered, just make some steps up from the inside & out past the trench and hop in and out, usually on 2-3 sides. They get broken occasionally, but not often. Before I do this I put down nothing, no fires or anything else that points to this as being a base. Ergo, no interest from the locals usualllly.
I set a workbench at ea corner then get in the build menu and start running around to see where there is any area without coverage. Carrying around the smallest wood floor piece works really well for this. You can see the radius of ea workbench as you move around. This I do with great diligence. Find the holes, drop a workbench and move on. Not until all this is done do I start building a base. It takes a little time but you have lots of room for a nice base w a couple buildings and plenty of garden space.
If you do it correctly nothing can spawn inside. If something does then it's not the game's fault. And every so often I go around and ck for problems. Especially after you start to get "A cold wind from the North" tho I did have a random blob that popped in unnoticed.
Sorry - wall of text.
Also, all the fun of mods feels problematic to me. How many players have problems with their mods and complain about the game being buggy, sending in bug reports, complaining on forums. After the game is finished then mod the squeak out of it, but EA really is about just playing it as it is currently designed and letting the dev team know what needs to be improved. They have a vision. But they do need to hear from us about how we feel about the game, tho steam forum maybe not the best place for this. With that being said, I portal metals to a second seed, lol not a purist.