As far as I know jumpseat(ing) and non-rev(ing) are 2 separate things...
A pilot can ask GA to ride in jumpseat - in which case GA will not put the pilot on stand by list to clear as non-rev.
Being a non-rev carries the risk of not being on the flight if its overbooked so sometimes pilots will proactively ask to ride in jumpseat
BUT in case the pilot instantly morphed into a non-rev as then he will be entitled to 'best available' seat per contract which in this case happens to be 3B.
I'd say the pilot had his cake and ate it too!