Most likely since her throne world is a pocket dimension, similar to the awoken home land. So one they secured the traveler, they could have easily sealed their pocket universe off. I've suggested, pre WQ, that the humans should just take the traveler into the awoken realm and destroy the portal.

Yes, The Witness can't get in , Rhulk was stuck in there For some reason the Scorn and us could go back and forth, maybe because Savathun didn't account for them has they are a recent development, and she counted on us being an ally The sad thing is, guess who provided us Deepsight, the Witness, so we could stop it, if Savathun completed her ritual the game is over, and the witness would have lost Which is why it's asinine at the end we say we are going to stop the witness, but in reality we just threw the game for it