I always had quite a different theory on this. Basically I thought that there are different types of invincibility: one type from grabs and one type from hits. Whether or not something will beat a super (or any move) depends on the properties of the invincibility.
For example, an SRK beats all throws, but can be meatied. Shippu on the other hand can be grabbed or command grabbed, but no regular hit will beat it. The startup interval of the move they do can have no invincibility, invincibility from throws or hits, or both.
Shippu has 2 (some say 3) frames of startup, and I believe a standard grab has 3. Provided that you throw at the right time, you can grab them before the shippu startup finishes (thereby grabbing them before any hit frames connect), but no regular hit can ever be timed to hit Ken out of it. Uppercut supers seem to have full invincibility (reflecting the throw invincibility of regular uppercuts).
I might technically be incorrect, but based on what I’ve seen, I think the theory works well enough for me to keep believing it until someone who knows for sure explains it.