TVAD,
I believe if the system we're listening to is transparent enough we will definitely be able to hear general and sonic characteris/differences between each unit and what one unit does better (or worse) than another.
From my personal experience I would say that over the years I've agreed with about 90% of what John Atkinson of Stereophile has said about the pariticular sonic characteristics of individual gear (of course after listening to it in my own system). And ususally John listens to a piece of gear in three or more different systems before making a final assessment.
Now your point as to whether or not these particular sonic characteristics are desirable or make "improvements" to a particular system are valid. That will be up to the individual to decide. As you've always stressed through out your posts, no one should buy anything before they've had a chance to audition it themselves. This shootout is only a guide.
However, I will say this (and your opinion may differ). If I am fortunate enough to get a really great piece of gear that's a reference piece and is known to have set a sonic standard in its class (i.e Halcro 58 amp, etc), even if it did not sound good in my system I'd probably abandon that system and re-tool it around that piece.
I believe in working around the strength of one's system and tailoring it around the component (or components) that bring the most to the table. Any system can be properly synergized to reach its maximum potential. Its just a matter of finding the proper fit of components, cables, etc.
Just my opinion!
AVGURU