I know some rod builders who swear by attaching the guides directly in line with the spline, be it on the soft or stiff side. This all depends on whether you want the rod to flex better on forward or back stroke, or to bend easily into a fish or give more leverage.
I also know rod builders who say that they line the sections up to be straight as possible and then place the guides accordingly. I have noticed that when you spine a blank properly, sometimes the sections do not line up straight, looking along the blank.
I also know that a well known blank manufacturer states - if you attach a 1 ounce weight to a the end of a blank the spine is unnoticeable.
I think that there may be advantages to playing with the guide placement on a spey rod. The sections on a spey rod get pulled in various directions during all but the overhead cast, and guide placement could be altered from the norm to maximise a rods potential for different casting styles. In fact, Bob Meiser's website has an article where he suggests that any rod builders try to play with the guide placement for this very reason.
This argument will rage on amongst the rod building fraternity, until somebody invents a machine(for consistency) to test if the tracking is affected by guide placement in relation to the blanks spline.
Does any human really notice a considerable difference for anything other than competition casting?