Exactly. If you actually own the cd, which I assume the threadstarter does not (correct me if i'm wrong), the soft, you will hear that the quiet part of the next song really fits actually.
It's probably because it's a ridiculously frustrating song and they cut it off before they went into a huge metal explosion which the song really needed, which would ruin the 'all-clean' nature of the album.
It still seems to me like they stunted the real growth of the song just so it would conform to fit that album when they could have either said 'fuck it' and put metal in it or just put it on Deliverance instead.