just one clarification : yes, it is physically possible to intonate your strings at fret 0 and fret 12 at 100% precision. There is no reason why that wouldn't be possible.

Now, if 0 and 12 are perfect, other frets might be a little off. It means your frets position is faulty... or your neck is bent in a weird way.

And thanks EBP for all the great advices, I've never thought about all these details