Woo-hoo! I'm so pleased someone noticed!! One "feature" of this kit is that it has a three-start thread, so two times out of three, the grain won't line up.
Also, if you take the cap off the nib end and stick it on the final end, clearly, you've reversed the body of the pen, so teh grain won't line up. BUT (I discovered this quite by accident) if you're sufficiently OCD, you can unscrew the nib and unscrew the finial, swap them over, thereby reversing the pen body and when you screw the cap on over the finial, the grain matches!!