I completely agree and came to support this.
When you romance him and ask him if you're going to talk about what happened he says that we are communed with our minds entire at the deepest level. The narrator said that now since we are bonded, Tav can truly understand The Emperor. I just feel like if we are connected at such a deep level this should be recognized in game as the OP's post suggest and The Emperor should want to keep us around even without fully transforming. To add he has Orpheus' power at the end so what if he stuck his own tadpole in our minds? I see that Duke Stelmane is mean to be his "flaw", however Astarion can sacrifice 7000 men, women and children, and a lot of people don't bat an eye when they choose that option. I am also quite jealous of Duke Stelmane as Tav because all he ever does is speak highly of her and praise her. She wasn't even infected or a mind flayer.