I would think that is the proper way. One would think the yeast needs to get at the raisins at its strongest point... primary. In the secondary how much yeast would really be active enough to get to the raisins.
Raisins in the primary add tannins and nutrients for the yeast. I've also read it enhances the body of a wine.
I had not thought of adding a few raisins to applewine.