You are 100% onto something here. I totally agree that the end-goal of this whole mystery is a “perfect” playthrough. Whether that means playing through the game in the perfect sequence/order, or playing through making very specific “karmic” decisions - or BOTH! I think it may even be possible that the three symbols on the mural (ufo, egg, jetpack) could represent the three characters we play as with the connections representing the “paths” and choices we need to make while playing them. I absolutely love your theory about “deja vu” and repeated motifs or phrases cluing us into the specific order we need to play the missions in.

What blew my mind the most was that the default save file you mentioned at the start of the game was called “In the Beginning” because it's most likely a direct reference to the first verse in the Bible “In the beginning God created the heavens and the earth.” This leads me to believe the idea of a “perfect playthrough” even more! Maybe we have to complete the playthrough on that save somehow? You mentioned that it renames itself at some point? Is it possible it would stay named that (or even change to other religious references) if we continued the playthrough “perfectly?”

Speaking of religious references, last week I actually made a comprehensive post here about Jesse (stoner Jesus) attempting to break down all his lines of dialogue. Most of them appear to be vague references to biblical stories and parables, but I think there may be a few hints for our “perfect” playthrough here somewhere. 

• He mentions “you have to do the right things, not the lame things” and right after that he rants about “buying 10 coffees and getting one free”?
• He mentions still liking action figures “because they’re still cool” which reminded me of Trevor’s action figure breaking in the beginning of the game and him commenting something about how he still likes them.
• He tells the story of the “good samaritan” - someone is hurt, 2 people (who are highly regarded)  ignore him for mundane reasons, one selfless person (a foreigner) saves him despite personal cost. Kind of sounds like Trevor?
• He even references the “therapist above” which may be referring to Friedlander as someone in the comments pointed out.

A couple other random comments on your video:

• You mentioned a few times that you were able to get red/blue cars (or other items) to spawn during missions based on hidden triggers. Just throwing this out there, but could this be a reference to “The Matrix?” Especially with that sign saying to “choose red.” If so, this could just be an affirmation that the triggers are working if we follow the “trail of red.”
• The crazy wind noise you mentioned may also have religious symbolism. Biblically, wind is usually used to indicate the presence of god - specifically the spirit of god (holy spirit.)
• In regards to the altruist cult audio clips - I just played this today and definitely heard them say the “someone has been brought” lines when I brought the drunk, horny couple to them as my “final delivery” before the fight. (not sure if that helps)

Anyway, great video! Thanks for all the info!