There’s still some weirdness: sometimes, both characters are relatively close to each other, and all hits connect. Sometimes, they just don’t. This often makes Ryu vs Ken/Ryu random, since full super vs 1 hit + either reversal shoryu or 4 blocked hits is a huge difference.
My guess is a mixture of two components, perhaps only one:[list]
Since the super does not move pixel by pixel, there might be precise distances where the super hits the extended arms with just a single pixel overlapping the hurtboxes. This gives slightly more room for the shoto to recover from the attack and either block or reversal jab shoryu;
Some weird scrolling effect such that if the screen does or does not scroll, then the full super will connect on a mid-screen shoto target with extended arms.
As for Sagat, I feel the super being blocked is pretty fair, and very unfair against O.Sagat. The latter can really just spam low tigers and not really give a shit about the super, unless he couldn’t get a big life lead by the time Ryu gets bar. Even the full super doesn’t do that much damage, since he has more damage reduction.