The X axis is not time. It is just the index into the array. The FFT Of Selection Over Time filter does not compute the frequencies, so the plot just gives you the indices of the array holding the values computed by the FFT. The frequencies wouldn’t mean much anyway since the the vtu file series does not properly mark time anyway.
Since both FFT Of Selection Over Time and Plot Data Over Time are using array indices for the x axis, and both arrays are the same length, they look the same. But they do not have the same meaning.