As I said in my initial post, these things are not universal, just because Erron's kicks can't go through, doesn't mean someone else's can, and same for punches.
But as I also said, the issue still comes around to character attack hit boxes, NRS should fix the disjointed hitboxes on these attacks, thus solving your issue, and making footsies much stronger. So regardless if I'm wrong about the clone itself, that still is the best way to resolve this, as I see it.
Also, you can mix people up from a safe range in the corner, use D4 for your low attack, then on hit go for your next mix up.