Even though I doubt the writers had that in mind, it certainly does clear up the 'boo-boos' and makes it more understandable.
Actually, at least some of the writers must have been aware of the implications of creating a new timeline upon sending a character into the past. The evidence for this would be their concept of parallel time in 1970.
I have a question though. Would Jeb Hawkes be from PT 1796 II? Since the ghost of Peter Bradford came back and said Jeb killed Vicki later on in the series. Maybe he went from Parellel Time II to the original time line?
This is a bit of a messed up story since they originally intended the ghost of Paul Stoddard, not the ghost of Peter Bradford, to confront Jeb Hawkes. And yes, it would have been Jeff's ghost from parallel time II, since that's where he and Vicki wound up ultimately. It's possible, however, that the Leviathan existing in the original timeline as well; the ghost that appeared to him was from an alternate timeline, but this Jeb may have been from the original timeline (and had no idea what he was talking about.)