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@dooks
Haven't read the article linked to yet but would also add that if you tune the open g string to be exactly in tune in an open g chord, it'll often sound sharp when you fret it at the 1st for an open e chord. I suspect most of the mismatch is caused by the effect of fretting so near the nut pulling sharp as opposed to any inherent equal temperament/fretted instrument compromise but it's been noticeable to a greater or lesser degree on almost every guitar I've ever played. I usually tweak tuning depend on what key i'm in. Most of the time that means tuning the G a fraction flat. One of the three Gs in a G chord being slightly flat is much less noticeable than the single slightly sharp G sharp major third in the E.
that's my logic anyway.