Tregoweth informs me that the Manson song was removed from later pressings of the album. It was supposedly made as a hidden track in the first place so that they wouldn't appear to be glorifying Manson.

I don't think Guns 'n Roses considered an album of punk covers a bad move; they considered themselves (and the critics considered them) one of the most punk of metal bands. Appetite For Destruction certainly stood out as different from the Poison and Whitesnake that was the state of popular heavy metal before its release. This album was a return to all of their roots after songs like "November Rain" which was Axl Rose's baby (before it was even recorded, he was quoted in a magazine as saying "If it doesn't get recorded right, I'll quit the business") and not really what the whole band wanted.