I guess I did a poor job making my comments. I agree, we cannot re-tune instruments on a recording. I am not assuming that we know some (not all) instruments are out of tune. I am saying this recording is being used as our reference and we don't know some instruments are out of tune. If an orchestra is fine except the string basses are out of tune, it will just drive us nuts and we won't know why. The problem is hidden among the other instruments. Not everyone has good hearing for pitch; most of us don't, unless we are professional musicians, and then the off pitch is masked. The sound is not going to sound quite right, and we will try to tweek the system to make it sound better, not perfect. We'll never get there because of a few out of tune instruments.
I think some have asked what we use as a reference. I wonder how much time we all spend tweeking this and that, and the problem is not our systems, but the source material, whether some things out of tune, or just bright, dull, or poorly mixed. Garbage in, garbage out.