I have noticed that the core rooms seem to have a greater chance of "randomly" being closer to the entrance, and I have wondered the same thing, but I always cleared the whole mine just in case. If you haven't found the queen yet, those markers seem to occur more often in the giant rooms that tend to be down in the basement. Although I have come across the occasional core or seal fragment in the open along a wall down there too.

So while it seems the odds are front loaded there, it's still a good idea to check the whole thing.