I think you might be reading too much into the films, to be honest.
Somehow, I doubt that what was on Yuasa's mind when he was making those films. They are just kid's films after all - nothing deep or profound there. (and certainly nothing sinister) They're simply entertainment, and that's it.
I apologise if that came off as being rude,- not not flaming you or anything - but I often wonder why some fans try to read between the lines when there's really nothing there to read.
I remember coming across some article going on about gay subtext in Godzilla vs. Megalon. I mean,
really.