Yes, their are different ways to tune and yes they can sound better depending on where you are playing on the neck and yes having your guitar's intonation properly set is important, but even that can be fine tuned, ( really detuned ), for an overall improvement and that is something that will vary somewhat from guitar to guitar and person to person. This isn't a new problem, it's as old as Western music and stringed instruments, ( Blame on the ancient Greeks ) it's because the octave is divided imperfectly into 12 equal half steps, the system we call "equal temprement", if you look at pictures of old Harpsichords from Bach's time, you'll see two keyboards, they couldn't play in tune in all keys for the same reason , maybe a double neck guitar is really the solution? When the piano was invented they "fixed" the problem by slightly detuning the strings just a tiny bit, middle C on a piano is normally a little sharp. See their is a simple answer to everything LOL, Whats the solution to the problem? Tune the best you can and live with the results, Hey not being perfectly in tune never bothered the Stones, maybe thats where the idea for "Satisfaction" came from..........