This one is maybe not a biggie, but it annoys me, so I'm posting to report it, or have an explanation why S3D behaves like this.
Look at this image:
This is just a test model of a cylindrical shape which has some very shallow (0.6 mm tall) cutouts in it (towards the printbed in this case). These cutouts somehow affects slicing (both infill and solid layers in the cutouts themselves), even if the cutouts in reality are finished printing after layer 2 (with 0.3 mm layer height). In the attached factory file, it prints solid layers up until layer 5, and when the infill starts at layer 6, those cutouts from the first two layers are still messing with the infill. I know there are ways to work around this by splitting into multiple process, but that shouldn't be necessary here, in my opinion.