I wish there were an "up vote" for this topic. More than 80% of my prints have a flat surface at some point and then additions projecting up. The projections have a weak connection because there is never a perfect overlay between the inner perimeters on the solid top layer of the flat surf...
I will concur the the desire to have a better alignment between the units used for the variable settings wizard and the slicer. Every time I have needed to use variable layers I have had to iterate at least four times. slice with a single process and then step through slices to find the target layer...
I may be seeing a similar issue. I designed an effector for a delta printer. It has an open center. I set the print to 100 infill so it is printed "solid". When Simplify3D slices it, the center opening is filled in. Cura and KISSlicer proces the STL correctly. STL: http://i.imgur.com/qOBmT...