To answer the original question GT instructors typically do the best they can with whatever resources are available:  live videos or official "canned" videos, authorized notation-tab books, just plain old figuring it out by ear.

On some of the older videos the production wasn't as good without multi-cam angles.  This is one reason GT tried to continually reshoot older material with updated production standards when it was possible.  Other times there were judgement calls or creative license decisions made by the instructor to get the lesson done in the most effective way possible.  For example if there were multiple overlapping guitars in an original recording, but the instructor was trying to make a logical composite path through the song to teach it.

Addressing this specific song lesson, it's an interesting case because I don't think either of them are entirely correct (GT's Douglas or Richie).

If you listen to the original version you'll hear there are 2 guitars.  Makes sense as JP was a 2 guitar band.  On most of the verse you can clearly hear one guitar emphasizing the upbeats of the E power chord rooted at the 7th fret.  This is what Douglas does, but Richie does not.

And you also hear another guitar playing the low E palm muted 1/8th note chugging in between each E power chord.  Douglas does not do this, but Richie does.

My best guess is that these parts were split amongst the 2 guitar players in JP.  And only one of them is Richie's role when he plays with the band.  Douglas might have left this part out thinking the other part was more crucial to the song or prominent in the mix.  Obviously I can't answer directly for him, so I don't know for sure.

I'm guessing if this lesson was reshot present day it would contain 2 separate guitar parts.  But if you are a single guitarist (alone or in a band) you'll have to make the call as to which part you want to play.  You can play either part.  Or you could make a kind of combination of the two.

Hope that helps.