If you want to mess with your brain, tune your guitar to a chord,
I just bought a 1997 Rickenbacker 330. It was a case queen under someone's bed for years. I had do to the normal work on it: new strings, bridge adjust. Other than that, the guitar is pristine,
I put a set of Di Dario NYXK 9s on it. (It has 12s). Tuned it with my Petersen Strobo Tuner and it sounder like crap. The intonation was sooo bad,
I dropped the needle on some Tom Petty and was off by a fat 1/4 semitone. So I tunes it by ear to TP, checked my harmonics, and then put the tuner back on just to see how far off. Dead nuts on!
I've been playing it all this afternoon, and it's spot on. Plays and sounds like a dream.
Not to say that the new strings, and acclimating to the new environment, but I'm tending to agree that the "sweetened tuning" is all in one's ears.
For no reason, All my guitars, except for this, the tuning is dead on with the tuner.
Maybe it just needed some time to adjust,