IMO, it depends on what you mean by internal logic. We know for a fact that people, and to some extent animals, do not always (and sometimes rarely) act based on what is logically the best choice for them. You then multiple those illogical choices across the millions of lifeforms (particularly sentient ones) and, IMO, it really breaks the idea of "internal logic."
Also, I find it the height a hubris that a single person (the DM) could reasonably determine what is "internally logical" in a campaign world let alone the vastness of the Multiverse.
Now, I do want to be clear that I do pretty much the exact same thing that you (and
@Micah Sweet) do. The only difference, if there is one, is that I acknowledge it is not the world's internal logic but the logic, parameters, constraints, freedoms, etc. that I, the DM, construct. And that does not mean it is anything close to a RL world (even if that is my intent). It just makes sense to me and my players and that is all I am asking for.