I have been trying to perform the intersection of a tapered cylinder with spheres to create holes in the tapered cylinder. It works but with artifacts. Specifically, the boundary of holes is sometimes locally linear or has knots in the boundary curves.
Here are two .brep files. One with a "tapered cylinder" and 3 spheres, and another with only 1 sphere.
May I request you to perform an intersection at your end? If you also observe similar behavior, what are the ways to avoid the artifacts?