As Muddy Waters infamously once said at a session in response to a question about the notes he was playing for a slide guitar riff:
"... most of the notes I play don't have names!"
Listen to old recordings of the blues and, indeed, any early recordings of Appalachian old time music and it puts all those D,A,dd players who geek about getting the intonation on their dulcimers 'perfect' into perspective

You just need to know the difference between 'good' out of tune and 'bad' out of tune - and I'm affraid you can't teach or theorise around that as the 'knowledge' is only hard won through playing music - there are no shortcuts or roads to understanding - you just have to physically play, and play, and play, and play, and................ Until you can FEEL the space between major and minor.