Well, it depends on the spine and blade of the knife and how it tapers towards the tip. If it is completely straight all the way to the tip like a cleaver for instance, then no, it doesn't matter. But if it does have a taper like most knives and you need to angle the spine to get the blade straight then yes it does matter. If you move it too far to one side when flipping then you slightly change the angle since the edge gets closer or farther.
When you set it up and have the blade stops all set, grab a sharpie and make a dot in the middle of the middle blade stop then make a mark on the knife at the same point and transfer it around to the other side of the knife. Align the marks when you flip the blade and you know it will always be the same.
