The issue here is in the word 'perfectly'; with well tempered or just tempered instruments some intervals can be 'perfectly' in tune, though others aren't. when even tempered scales appeared (to my knowledge, with the advent of synthesizers), some sort of common ground was reached - with even tempering (that is, the same distance octaves divided in to 12 equal steps), notes can measure in tune yet not sound in tune. Once you apply even tempering to a fretted instrument, more variables appear: At best, a fretted instrument can be pretty close. Pressure has already been mentioned, and the condition of the string can also be a variable. There are LOTS of things to think about here...
Anyone besides me remember the fanned fret Dingwall basses? An aquaintance swears that those are the most in-tune basses he's ever played (and he's played on lots of records). I'd suggest that you intonate your bass as best you can and don't worry overmuch about it. With a digital tuner, I can see why it would be very difficult to get the harmonics on the 12th and 7th frets to perfectly match their fretted counterparts; I've always split the difference - if the 12th is a hair sharp and the 7th is a hair flat, I call it a draw and move on...
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