Yes the endgame feels.... Weird at best IMHO.
There has to be an option to be the hero without becoming an illithid. Period.
And that the emperor sides with the netherbrain if you want to free Orpheus is just illogical beyond reason. The emperor did everything to get rid of the elder brain. Why should he have any reason to side with the elder brain and be a slave again? Is Tav a bigger threat to him then the brain? From a logical point of view its nonsense.
For me with this ending all choices that led me to the end feels like it was only an illusion that my choices matter. In the end I became what I was working against right from the start.
Don't get me wrong the game itself is really enjoyable but this ending does not fit the whole journey...
I think you hit the nail on the head. In isolation, a 'cannot win without sacrifice' ending could work. The problem is that the story has to be set up for it. Whether it be by reinforcing a moral grey give and take theme throughout the game, establish early on that the hero was not expecting to get out of this one alive or what have you. What we have is at best a mood whiplash or a bait and switch. It's the same reason why Karlach's story does not work for many people. The ending she has is not set up nor justified, so it 'feels' wrong.
That's before getting into problems regarding the actual writing of the thing, instead of just the theming.