Why are several of the Tu-104’s cabin windows oddly positioned?
I found a cutaway diagram of the Tu-104B. It appears that, at least on this model, some of the seats in the middle were raised a bit to perhaps accommodate some engine parts (there appears to be a label on the diagram which I can't quite read). The windows were raised correspondingly to match the seats. The mid-positioned one at the aft may have been placed there to match one in a door on the port side of the aircraft. The three high-positioned ones appear to be windows in the toilets (туале́ты).