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Even at conservative focal lengths (900mm), I've never been able to achieve absolutely spot-on GoTo using the SynScan alignment routine.
Using your guiding camera in conjunction with the bullseye overlay in PHD will get you closer than doing it visually. You can do this by defocusing the star so that it fills the inside circle of the bullseye overlay -- that'll get you right in the middle assuming your optical train is centered on your objective.
You can improve on the accuracy of the Synscan alignment even further by using the EQMOD n point alignment model in conjunction with AstroTortilla plate-solving. By syncing the mount half a dozen or more times this way, slewing to a target will see it very close to the middle of the FoV if done correctly. The more points you add to your model in various parts of the sky, the more accurate your GoTo will be.
This is probably not applicable to you Raymo, but it should be said that an overloaded or poorly balanced mount will throw your GoTo accuracy.
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