This issue is the only thing keeping me from using simplify3d more often. PLEASE FIX IT!! I use slic3r because it has a solution for this that I would absolutely *LOVE* to see in simplify3d. I love everything else about the product. Let me show you what slic3r does.
Here is a demo part I made:
It has both a chimney and an inset. In retrospect, I should have made the inset smaller because it hides some of the problems. Here is what that looks like in simplify3d, just before the first layer of the chimney is printed:
Now the walls of the chimney will print just INSIDE of the flat roof area that was printed. This causes 2 different problems.
A) The chimney isn't well adhered to the part, as it only has the support layers and the edge it sits next to that it is fused to.
B) the roof leading up to the chimney doesn't have good support, so it peels back as the extruder changes direction.
Here is how slic3r looks on that same layer:
WOW! I didn't have to tweak settings, or do anything special to get this. It solves BOTH problem A and B. The roof extends further in to the part. This gives it some extra support along the edges because the bridging can reach more support edges, and the chimney has more to fuse to.