I do have a theory that all those spawn blocking objects work, but spawns may slip through before the object has loaded in. My base is pretty large and on a couple occasions it has taken so long to load in that I sailed right into where my dock is before it finally loaded, causing my boat to clip into it.

Another thing I have seen is pieces of my buildings randomly collapsed for no reason, leaving the materials underneath for me to retrieve. This has even happened with roof pieces that enemies can't reach. It could be a similar issue where the base is loading sections at a time, and certain sections are loading in before other pieces that they need for support.

As further evidence, I did notice that my base loaded considerably slower while I had these invasive and apparently VERY fertile tame wolves all over the place, and the in-base spawns got worse right along with it.

If that's the cause, then I can't think of any way for players to get around it.