I'm surprised that Simplify3D still cannot do different skirts/brims and rafts per-process. I'd like to be able to add a brim or raft to a tall thin part that's being printed at the same time as other parts not requiring a brim or raft.
This is already possible in S3D. You create 2 processes, one for each part. Then you can configure independent raft/skirt/brim settings for each process. The only thing to keep in mind is that the parts can't be too close together on the bed. If they get too close, the software will give them the same settings to allow things like dual extrusion to work correctly.