I think you are focusing too closely on the details instead of the big picture. Let's assume that Rook's mix-up is exactly as strong as you have claimed - it's overpowered. Now let's pretend that every other character in the game has a huge fireball that takes up the entire screen, pushes the opponent back to full screen, and starts up really fast. Is rook still overpowered in this pretend version of the game? No, right? It doesn't matter how strong his mix-ups are if he never gets in range to do them.
Ok, so you already understand what I'm getting at. Here's the thing: EVERY character has what you call "soft counters" to Rook, including degrey. They can use those tools to avoid his throws while still dealing damage. Then Rook will try to deal with those things with his own tools. That's where the game is! Rounds don't start with you knocked down next to Rook.
Rook deserves to get his "unfair" mix-ups if he's right on top of you. But in actual play, getting there is the hard part. That's why overall, consensus is that rook is not overpowered.