I agree with Simon that the bridge is skew-whiff.
I reckon if you rotate the bridge clockwise about 1-2 degrees, those strings will line up just fine.
You may still need to shift the neck a little too. The E6 and fretboard edge aren't really visible in the 4th fret photo.
Neck alignment has less noticeable effect the closer to the bridge you get, but every little bit can make a difference.
Ok... NOW... I'm going to say something that I will probably get flogged for but...
Perfect alignment of strings over pole pieces is not absolutely necessary beyond "looking better".
The magnetic field in which the string vibrates within extends well beyond the little circular area of the top of the pole piece.
You'd be surprised how many strats there are out in the world without perfect alignment.
And I would wager you couldn't hear the difference between one that is perfectly aligned and one that is not. If both guitars are properly set up and pickup heights are also adjusted properly, they'll sound just fine.