Just read through that now, interesting! Knew the theory existed but didn't know anyone had gone into so much depth about it. I never interpreted it that way but it is a good read anyway like you say. Have Square ever confirmed or denied that?
I think for a theory like that to come about shows there are some things with FF8's plot that could've maybe done with a bit of refining. I was so taken in by the game when I was younger that I just sort of accepted it, but it's only now when I compare it these days to something as perfect as FF7 that I see the real difference in storytelling. Still, apart from one major plot event, it's mostly smaller things as opposed to a whole chain of ridiculousness. I loved the ideas behind SeeD, the sorceress, the Gardens, Laguna's story, etc... The issues I have with the game weren't enough to take everything away from that, the card game and the junctioning system. It's still one of the best JRPGs ever, and it's more the fact that the FFs either side of it nailed everything all at once in my opinion. 6 collapsed slightly towards the end, 8 was maybe a bit too fantastical, 7, 9 and 10 were near perfect examples of JRPG storytelling.
Great games can still be such whilst having a big stumbling point, I think. I ramble on to no end about the second disc of Xenogears - it had one of the most amazing stories in any video game, but with an absolute catastrophe of a second disc. A lot more of a let down than the way FF6 slowed towards the end. Still, a lot of people maintain it's the best JRPG of all time. All things considered I'd say it's about the same standard as FF8 - a flawed gem.