I thought the O.P. was talking about the crankshaft/spinner not being centered, ie, being shifted left or right.

The problem you describe is seperate. I've seen some planes where the cowl front was at a small angle to compenstate, but for the most part, you're stuck. However, there is 1 thing you can do if you want to put in the effort. Set up the plane, get it all mounted, and flight test to make sure you get the thrust line you want for your engine/prop and flying style. Then add a balsa or ply shim to the front of the cowl and sand to exactly match the spinner, leaving a little space. Seal and paint to match the cowl, and you can get a perfect fit. If you really want it to be perfect, apply a bit of glass cloth over top, and do all that fiberglass finishing stuff. Labor intensive, but it is cool when you see a plane with the spinner so well fitted you almost can't see the gap between spinner and cowl.