All of this presumes that the audio engineer's ears and tastes are inline with what whatever audiophile "standard" folks in this thread hopefully applies. That just about NEVER, EVER happens.
Let us not forget musicians, engineers, and audiophiles are three distinct species, with the overlap of audiophiles and the other two being by far the smallest in the equation. Yes, there is a small movement towards those who publish things almost exactly as they were recorded, but again, it is a small movement. The industry has accepted certain bastardizations as being necessary to make music either playable on a car/table radio or saleable.
Recording engineers, like anyone working in a field mixing both art and science, leave as much of a fingerprint on the sound as anyone in the band. When you go to different restaurants, the same recipe will taste different because a different chef has prepared it. Music is absolutely no different. Anyone who hears the original tapes in comparison to the mixdowns knows the latter rarely lines up with the former. In fact, musicians seek out engineers to lend a particular flavor or "seasoning" to the end product. For example, engineers such as Brian Eno and Daniel Lanois have very recognizable sonic signatures. Lanois' work, characterized by his incredibly dark and heavy sound is as far away from what is originally put down on tape as one can imagine, yet he remains always in demand with the most well known musicians in the industry.
Bottom line, the way your system sounds is as unique as your musical taste. No need to fret over it, or feel you aren't living up to some "standard". Just go with it; whether "it" is the absolute sound of unamplified instruments or something different than that. No one is ever held to account as to why they drink Coke or Pepsi, why let them them hold you to something with your system and/or music? After all, the tastes of those involved in making and producing that music are just as varied as ours.