Turns out Shinji was just as confused by the last two episodes of Evangelion as the rest of us.
I actually asked Spike Spencer about this rant at AMA this year.
He said he just was so annoyed with the ending as he was dubbing it that he just told them to turn the mics back on just to let him record this.
“now, if i were to run away, let’s analyze that”
“where the FUCK would I go”