What did really happen in the end of Phantom: Requiem for the Phantom?
The anime ending is different from the visual novel.
Ein and Zwei were definitely together in that last scene because Ein was talking to him.   

The poisonous flower idea is a fan theory without official source. There are no official explanations of what happened in the last scene. It does make sense, though, to assume Ein committed suicide after Zwei got shot, and the flowers are the best and easiest tools for her suicide.    

Since there's no official explanation, you can go with whatever idea you want.