There are many stages to mastery on an instrument. But if we divide it into 2 (for the sake of argument) they would be:
- the years spent acquiring and internalizing the scales and chord shapes, intervals, sounds, progressions and all the technical side of it. The VAST majority of players never get near or beyond this.
- mastery - when all this leg work is owned and like second nature. These cats don't need to think like this any more (unless adding new pieces). they use their ears and simply play.
There is a window into this in one of Scott Henderson's videos, where he says "you gotta KNOW this stuff down. If you have to stop and think for even a second about where the notes are, you are not ready to tackle changes like this" (paraphrasing). He and other players like him, OWN this stuff. No thought, no theory, just expression, a use of all these tools.
I think most discussions of the different modal or key based (more theory driven) approaches to improvising over chords apply to the first phase (obviously). Where I get lost in these types of discussions, is when people start dissecting and analyzing what the masters do. What they do when they play I don't think applies. What they DID as they were approaching mastery during their endless practice hours is more what maters.
I think the time you spend really thinking about and using theory and all that, is the phase where these sounds get embedded in your ears. During the practicing of these approaches, where it feels very difficult and unnatural for a long while, leads eventually to hearing these sounds more clearly. The 'thinking' part fades away - THEN you can truly begin to express yourself.
Learning can lead to KNOWING...
Which is a lot better than GUESSING and HOPING!