The area I had the greatest issue with - and we are talking four engine airliner here - was where the nacelle shading met the underwing shading. A mate from Singapore who got into profile art via flight sim repaints had the same issues. Never found a satisfactory solution until I merged the wing and nacelle shading into a single layer. Might be problem exacerbated by scale. My profiles are only 3000px wide, so the critical nacelle/wing overlap is quite small on a DC-7, for instance.
Flattening the image is what we do at the newspaper I work at before the page is made up as a pdf file. It is to reduce file size but we are talking huge high res files here - several hundred Mbs before flattening. With a mainframe, file storage is not an issue like on a PC. I convert my images to a 800px jpegs for the crude pdf catalogue I can send out to interested people. When I print - and all my profiles are printed - I do it off the layered pdf file onto A4. Printing on A4 reduces the image to about 30% of the original without reducing the pixel count. Makes for very sharp images.
David