I had a very similar reaction. That ending was the one I got for my first playthrough and I remember being really confused about the epilogue until Ciri was revealed.
As for the thread in general, the empress ending is my favourite. To me, it makes the most sense, it's really bittersweet and beautiful, plus the different scenery is really enjoyable.
The sad ending I have never got, and never will. Too tragic for me.
