Frusciante is an amazing guitar player — check out his solo albums. He knew what he was doing putting those out of tune notes in.
replyOutside of people like van halen also pretty much no one is exploring the entire neck on a single song. So the issue of the guitar not being perfectly intonated is irrelevant since they are using just a piece of its range.
replyA lot of simple songs are just open "cowboy" chords for sure. But those are played on the first frets while the guitar is typically intonated at the 12th fret and tuned with open strings. I would expect those first frets to be fairly "out" vs. the open strings.
reply“Whole neck” is irrelevant. Things can go out of tune at any fret.
replyEVH famously tuned his B string slightly flat to make his D (on the 3rd fret) sound better. Look it up.