I know that there was at least one Rage that was programmed into the game that Gau never has the opportunity to learn because its counterpart monster does not appear on the Veldt or something.
As for the topic at hand, I have only obtained 100% by the game's standards on Final Fantasy X-2 because that is the only game that monitors completeness. I do not have the capability of meeting the fan communities' guidelines of complete games for the other titles in the series.