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This is clearly a bug in the game, and the error in the code logic is very apparent. Essentially, neutral zones are represented by -1, which indicates the end of the table, while the extra castle zones are represented by 0, indicating empty spaces after the end of the table.
My understanding is that the question primarily concerns neutral dwellings, pandoras, and seers, right? They shouldn't actually appear according to the original design; they are a result of the bug.
I have code that, in addition to fixing the bug, makes it so that, regardless of the terrain, a zone without a city has a certain chance of becoming neutral. If baratorch deems it necessary, he can include it in HD.
By the way, it would be interesting to know how multiplayer players feel about neutral zones. So far, I've only noticed that since that version was released, no one has paid attention to their absence. :)