When I say 'perfect', I mean 'absolute'.
If you're tuning say, your piano, with a strobe tuner, and you tune 'perfectly', it's never going to be perfect. Subtle differences due to the way metal strings, wood, etc. vibrate.
If you play two 'perfect' fundamental notes together they sound very harsh.
I'm not saying that warbling sound you hear when out of tune is more pleasant, I'm saying if you have them 'absolutely perfectly' tuned, it'll sound harsh.
Fortunately, outside of digital music, you'll never have true 'perfect' intonation, doesn't matter the instrument.
But that being said, even digital instruments take this into account and aren't 'perfect'.
With something like a piano though, because of imperfections inherent to the materials, if you try to tune equal temperament it seems to enhance the imperfections, making them more noticeable and much more displeasing to the ear. The same goes for most instruments, but to a lesser degree in some cases.
So let me rephrase my original statement...
'Absolute perfect' tuning can sound harsh to the human ear, 'near perfect' tuning can enhance the unavoidable imperfections in the harmonics and instruments are often tuned with deliberate variances in intonation to, in effect, mask these imperfections.
Make more sense now?