Fascinating posts, guys, deserving of a more serious response. I agree with blindjim that transparency is a much better term for what we are talking about here. Music is not, and never should be "neutral." As a professional musician, the term has always been hilarious to me when applied in this context. No musician wants to sound "neutral," that's for sure!
And Vandermeulen, no good engineer would start from some strange idea of "neutral," either. One of the reasons recording studios are so dead is because then the engineer can make the recording sound however he wants easier ("coloration?"). No real performing space is "neutral" - the room's acoustics always have a huge effect on the musician's sounds (natural coloration, if you will). If an orchestra is on tour, for instance, playing the same piece several nights in several different venues, there are constant adjustments made to account for the different acoustics. This is one problem with the concept of "the absolute sound." Which hall is supposed to be the example of this? There are a great many different answers to your final question - what is the music supposed to sound like? No two engineers or musicians will agree exactly, nor should they.
So to get back to the OP's point, then, I don't believe that "neutrality" should be a reference point. The reference point should be what you want the music to sound like, which for most of us is as close to "live" as we can get (and this will take the sort of study that Vandermeulen was talking about, to decide what you think it should sound like). I agree with blindjim, there is no such thing as "absolute neutrality" or transparency in a piece of audio equipment - there is always going to be some designer bias, whether he/she is even conscious of it or not - the equipment will sound how the designer wants it to.