More times than not I have found that you can use the cowl as a general guide to help you with proper engine incidence. Meaning that if the backplate of the spinner is not flush with the front of the cowl then it very well could be that your incidence is off on the engine anyway and it needs to be adjusted.

Personally I would be more concerned with proper incidence of the engine than the cowl and cone matching up perfect. If after setting the incidence correctly and still finding that the cowl doesnt match perfect you can make adjustments on the cowl. If you put down a sheet of sandpaper you can very carefully sand an incline into the back of the cowl so that it matches the angle of the spinner. But I would only do that after finding the exact incidence on the engine and testing it in flight.

Also, with some of the planes that I have built there have been things that I thought were a real eyesore (a wrinkle in the monokote, a fingerprint on the inside of the canopy, etc) I always think that I will go back and fix it but once I get it to to the field and fly it for a few weeks I realize that I dont really notice the ¨eyesore¨ so much anyway.