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...if the rim and wheel appear, as you say, to be otherwise true and intact, and it is a rim that has a hooked bead groove, I would personally just mount a new tyre on it and put it on the bike and ride it. If it rides OK, I would not worry too much about it. I have not ever (and I have looked at a lot of wheels) noticed something like you describe, but I can see where it's possible. Bicycle wheels are one of the more abused and generally misunderstood components in the cycling world.

If I had to guess at the cause, it would be a manufacturing blip, because I'm unable to envision some sort of mechanical damage that would neatly change the level of one bead seat versus the other for the entire diameter of your rim. I am likewise unable to envision a wheelbuilding error that would produce this result. Perhaps I lack imagination.