Yes, the point of this is to be able to take the STL file (with supports) into another application, for example another slicer. In my case, PRUSA i3 owners have a custom PRUSA version of slic3r with some custom features. I bought Simplify 3D assuming I could use it's awesome custom support features, then export to STL and slice/print using slic3r. Apparently that's not an option (like it is with Meshmixer, which also does great supports).
S3D staff: If you're listening, sadly this makes the software unusable for me, and I'll be requesting a refund. If you add this capability, I will happily re-purchase!