the NY players have spent a long time investigating this topic and there is one thing that needs clarification because it's a little off.
See, the characters that you're talking about that get advantage off their d3s operate like this: they get +10 on hit on a CROUCHING opponent but only +3 on a STANDING opponent.
This is important for the following reason.
When in vulnerable frames from a blocked poke, although they are in an animation that is crouched, the game engine considers their stand/crouch state based on whether or not they are holding "down" at that particular instance of hit connection. In other words, the input from the controller is what dictates which state they are in: standing or crouching.
For example, if you were to block someone's d1 and punish with d3, you're not guaranteed to be at +10. That depends on whether they HELD "down" after d1 or just tapped it. If they just tapped it, you will hit them in what the game engine sees as standing state and will only be +3.
If your character has a 9 frame or less special mid or low (Kabal f4, Cage f3, Liu Kang b3) you can counter poke d1's for full combo if you scout one.
For characters like my man Smoke, they don't have any normals like this so I always counter poke with d3 to get advantage. However, you won't know how much advantage you're at until you can see your opponent's hit animation.
This might seem confusing, but it's important.