Rule for questions like "Or is it?"

Your example is an instance of the rhetorical figure called metanoia: Making a statement and then correcting or questioning it so as to possibly refute it.

Examples:

If she come in, she'll surely speak to my wife / My wife, my wife! What wife? — Shakespeare, Othello, Act 5, Scene 2

No other should taste the happiness I scorn. Why do I say happiness? — Fielding, Joseph Andrews

We, like children, often assert things as positive when in actual fact they are a little less than absolute truth, or even false. Posing a question after an assertion this way is a very strong way to indicate a truth value somewhere close to the middle, a truth of which there is considerable doubt [nowhere near absolute]. It introduces a certain state of mind in the reader.

In that sense, you are right. The initial belief is proved wrong later.

A positive statement is stronger than a negative one. So "Or is it?" introduces more doubt than "Or isn't it?" although both do mean the same.