I waded through that article and at least I now understand why it all seems so murky. LOL. However, the relevant murkiness seems confined to the final part of his service and it's not clear that he ever actually failed to do anything that was required of him. Or am I missing something here?
Not really- the way any military unit is structured, you have to be present & accounted for, or your absence excused through channels. If President Bush had, in fact, not reported or walked away without proper protocols, the Air Police would have hunted him down & returned him.
There would have been no honorable discharge, either.
The "murkiness" you note- sloppy paperwork- is not uncommon, especially so many years having elapsed.