Don't ask me difficult questions...
I'm in the (confortable) user side.
I would compare mplayer and ffprobe output, and in case of discrepancies, ask for user input. Of course it may lead to errors, it's better to offer a single solution and not depend on variable user skill or taste.
I assume that sometimes a bad PAR encoded signal in stream may be corrected with a correct PAR signal in header, isn't it?. Or will PAR in stream be always correct?
As you see I have no skills in this matter, just from the user point of view. Just thinking in loud voice...