The director of the film wanted a song like "Careful with that axe, Eugene" because the final scene in the movie is dramatick, and so is the song. The song starts just after the same house has exploded a couple of times, and when the song is playing, there is a lot of other things that explodes. So, the people who watches the movie, is moved away from the 'original' scene and is watching all this other stuff exploding. After the screaming part has begun, the music stops for a while when we can see Daria getting in to her car and driving away, smiling. And then the music starts up again and is played to the end.
The main differents in these two songs (Careful.. and Come in...) is that "Come in number 51, your time is up" is instrumental. The song does not contain the lyrics "Careful with that axe, Eugene" just before the intence screaming starts.
My personal opinion: I live both songs. The line "Careful...." would not be suited in the scene in the film, and it was perfectly ok that they choose not to use it.
Antonioni 'found' the song while the band was recording "Live at Pompeii" He loved it, but it also made him feel sad, like he was in a church.
The clip I found, you can see the house I was talking about, that explodes! And you see all the other things that explodes during the song.