My Spoiler 4 has the same 'misalignment', especially on the E string. And a similar thing happens on cone headstocks, where the tuners are supposed to be aligned with the slots in the nut, but still you see that the string doesn't bridge the gap in a straight line. I think it doesn't matter too much, as long as there is no extreme deviation - if you look at the crown headstock you know it can't really be a problem.
Another alignment puzzle is the positioning of the oval inlays on the fingerboard, which appear to be a little off-centre, biased to the lower strings - but I suppose that's what you get from not using a machine to do that kind of work.