Don't forget that the isolated guitar tracks are often/usually/mostly post-mix. Meaning what is isolated is the sound after the engineer has worked his craft, chopping here, boosting there, etc. This has then little to do with the original tone of the guitar as it sounded coming out of the amp.
So when you "tone-match" an isolated track and say "that's what the original sounds like" well, no, not really. That's what worked in the mix with that specific bass track, these drums, those strings and synths, etc.