I know what string length changes do, and how to use them. But no amount of saddle adjustment can make every fret line land at exactly the in-tune spot, across the neck (with typical frets, which span all the strings in a straight run). You simply cannot perfectly tune every fret on a fretted bass, nor every line on a lined fretless. The only way you can do that is by having the frets in different locations for each string.
Of course, as I said before, lines do not prevent you from having perfect intonation, or warping notes however you want. Just because they are there, doesn’t mean you have to play right on them. It’s just that the lines will naturally draw you to them, and you have to be more deliberate, and/or get over having your fingers glued to the lines (which is not much better than playing fretted, in terms of intonation).
Or, to say roughly the same thing in another way...what this guy said:
Are you aware of different tuning temperaments? Because that is, I believe, what you're referring to.
Anyone who says a fretted instrument is not able to be perfectly in tune is speaking in regard to a specific temperament.
By your logic, which is not wrong by the way, piano is out of tune with nearly every chord played.
However, according to the temperament used on fretted instruments, the fret lines are perfect for their perfect division of intervals.
But yes, in advanced music we learn of the tuning details you're talking about.
But keep in mind... unless you're playing with other musicians who are tuning outside of equal temperament, then you'd better play exactly on the equal tempered notes (ie... using frets or exactly stopping at the fret lines) or you'll be out of tune with the other instruments.
The tuning issue you're talking about isn't normally a true statement for most of us who are playing with guitarists and keyboardists much of the time.
It does drive me crazy though how a tenth is often sharp on a guitar or bass.... and I too like being able to play double and triple stops using perfect interval tuning on fretless.
But saying the frets or fret lines are out of tune is vague and inaccurate without further explanation since it is perfectly in tune for the equal tempered scale on each individual string.
I used to hand tune my music school's harpsichord to certain keys for certain performances, because that was how things were done back in the days before pianoforte. It's a bizarre thing to hear these days on keyboard though, since we're accustomed to equal tempered piano.