Okay, Christian here, and this are some ridiculously tenuous connections. At the very best case, and Game Theory is entirely right here, we've got Neon Genesis Evangelion level "random symbolism makes everything better" stuff.
(Disclaimer, I played Crono Trigger through once a few years ago, so I don't have perfect recollection, so I'm using a summary to aide my memory)
I was going to go point by point and point out all the flaws, but, this might be more fun. I present to you:
THE GOSPEL OF JESUS, According to Square Enix (according to Game Theory)
Jesus was born to a virgin in some time period after the Crusades; after some time traveling back to the Crusades to rescue a princess, in the defining action of his life, he's suddenly betrayed, put on trial, and sentenced to death for a crime that... well yeah, he actually did commit, but hey the punishment was still draconian... anyways, he's betrayed, tried, sentenced to a (somewhat) unjust death... so he breaks jail and kills a dinosaur.
So after skipping prison, Jesus and Co. travel forward in time, where they see one of the signs sent by God to signal Jesus's second coming, (except that the sign was sent 65,001,999 years too early so it chills underground) and are determined to prevent it. So after picking up another disciple, and a brief pitstop in the Old Testament where they pick up Moses as yet another disciple, they travel back to the crusades and Peter fights Saladin with a magical sword given to him by one of the wise men. (Only after Jesus wanders around killing Muslims for awhile)
Having done that, Jesus, Luke, Mark, Peter, Robo, and Moses travel to [what by process of elimination must represent] the Middle East in the time of Christ, and after [a bunch of stuff that has nothing even close to resembling a Biblical parallel here], Jesus realizes he missed a great opportunity with that betrayal, (almost) unfair trial, and imprisonment earlier, jumps a bullet.
At this point, the disciples including possibly Saladin, might bother with bringing Jesus back to life, [but that's optional since the Resurrection of Jesus obviously wasn't like the entire point of that story or anything] but if not they'll travel to the future to destroy that sign of the apocalypse (sent by God 65,001,999 years too early), which at this point also represents a completely different sign of the apocalypse involving a woman and a 10-horn beast. Unless they don't.
So yeah; I'm going to say if they were trying to tell the story of Jesus, they probably should actually read it, instead of just basing it on what you learned from a couple scattered pages of the CliffNotes version and the Charlie Brown Christmas Special.
More likely, we've just got a developer xeroxing apocalyptic symbolism from the book that gives us the word "apocalypse" (which is from a greek word that literally means "a revelation", hence the English name for the book of the Bible). Nothing wrong with that, but it's not nearly as deep or as interesting as this video thinks. Crono = Jesus really doesn't go farther than "heroic sacrifice", and it's done for the wrong reasons and with the wrong result.
So, if you want to see a non-standard depiction of Jesus in a post-apocalyptic setting? Just go watch Trigun.
-LOVE & PEACE!