While I can't say why S3D keeps looking for overhangs when support generation is disabled (bridging?)... I can guess why it's taking
ages. I had a look at the STL (after exporting it from the factory file). It reports as 9838 Shells... so to S3D this is the same
when slicing/preparing as close to 10k single objects on the plate....
Looking at the model I wouldn't be wondered if it's really 10k single boxes, not properly added to a single body/shell. Slic3r/Cura do
some mesh optimization/reduction while importing - maybe that's why I can slice this in Cura/Slic3r...
Had a quick look at the STL in Meshmixer. But that one is having problems handling 9.8k boxes as well... (tried to Join them, convert them to boolean using Make Solid...). Remeshing does work but doesn't look very pretty....
Thousands of boxes inside others.... ^^