I was just about to address this.
Erm, yeah? Gen 1 data structure for Pokemon is really small. It doesn't contain origin game byte, for example.
So PKHeX is really taking best guesses here. If it's a Bulbasaur with no egg moves, and has no moves to suggest it learned a move early (cause Gen 2 might have changed the move roster via leveling around), PKHeX has no way to identify that a mon was bred in Gen 2.
TL;DR: For Gen 1/Gen 2 entries, if the mon has no identifying features to show it was bred in Gen 2, and the mon is in a Gen 1 save, PKHeX would not think that it's bred in Gen 2.
Basically, there is no specific byte in the data that labels the mon as a Gen 1 mon or Gen 2 mon. What determines it, would be the circumstances surrounding it. (Such as what level is it at, what moves does it have, what game is it in, caught location [only applies to Crystal], etc)
Also, please stop multiposting. If you got any new information, and your latest post is unanswered, edit the information into that post.