Yes, you should answer "NO" to the question as to whether you overfunded your return.
What the question really wants to know is "Did you carry over any excess from the previous year?" Since you cured the excess by withdrawing it in a timely fashion, you did not carry over anything. This is why there is the reference to form 5329 - if you had carried over anything, it would have shown up on the previous year's 5329.
The question could be better phrased to avoid confusion.
I am glad my answer from way back when is still good. 😉
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