With the stuff I am familiar with, wavy is normally problems with fiberglass molding, etc... There is something differential going on, and it comes out in the hulls. Nomally that doesn't happen with strip since it has a firm base of wood which has the advantages of a core, and further longi stiffness of a wood. You can have other stuff that prints through on wood when the boat is older. For instance the difference in areas with a lot of compound near no compound, or only cloth, or some different grain. The less the glass, the less the putty (whole hull foat and sand out), the more the possibility of print through, and doubtless other stuff. It does get more difficult when you build to ultimate light weight.
Fairing won't take care of it, but I know what you mean, you can shave it down at that time, or ignore it since the variance is pretty small.