A major problem in your question, I think, is that 'transparent' is a qualitative term. It is subjective. As such, it will be defined differently by different people. An audio equipment engineer needs a quantitative definition of transparent in order to engineer transparency in to a product. He/she needs a set of numerical specifications to meet. The assumption here, of course, is that meeting some set of numerical specifications will produce subjectively transparent sound. But, will it? Many components today deliver nearly perfect specifications, yet often fall well short of sounding like real instruments, or, more importantly, communicating emotion. If the subjective system result is clinical sounding, what has been achieved? If the original musical event was not clinical sounding, yet the electronic reproduction by equipment having nearly perfect specifications so often is, might it be valid to view this clinical sounding reproduction as being colored in some respect? After all, music is not appreciated by lab equipment, it is only appreciated by human beings. If an serious audio system does not musically communicate joy, or sadness, or some emotions which can't even be described with words, what exactly is it's purpose?
My experience is that the gift of music is it's ability to communicate emotions in a way that no other human medium can. Music doesn't simply tell the listener the emotions of the musician or of the composer, it can cause the listener to actually experience those emotions for themselves. This being the true gift of music leads me to conclude that emotional communication is the first requirement of any serious audio system. If some form of qualitative coloration is involved in conveying emotional communication, especially at affordable price points, then so be it. I feel that highest form of home audio reproduction occurs when a system seamlessly merges emotional communication with subjective transparency (the lack of percieved coloration or obstruction). In this too rare case, there is not the dichotomous choice of emotional communication or transparency of presentation that is dictated by the great majority of audio gear.
I feel that gear which only delivers objective transparency (excellent specifications) occupy the bottom most rung of the musical satisfaction ladder for a serious audio system. Next up that ladder is subjective transparency. Subjectively transparent systems are often interesting to listen to at first, even sounding like live instruments playing, but eventually, they become surprisingly uninteresting for their lack of emotional communication. One might think that a transparent sound would naturally also convey emotion effectively, but for some odd reason this often seems not to be the case. Next up the ladder is emotional communication, which I feel is the lowest acceptable level of performance for any serious audio system. Finally, at the top, is emotional communication combined with subjective transparency. These rare systems not only often sound like live instruments playing, they consistently move the soul as well. The technology simply fades away from concious awareness, and what's left is the music. No restless analyzing of th sound. No distractions. This is the audio system holy grail in my view.