I can't tell you if using raster images with spot colors will work in Flexi or not. I use Omega and it can certainly be done there providing you have a separated image for each spot color. Then it's a matter of layering them in the order you want them; setting up overprints, chokes, spreads, bleeds, halftones and LPI settings. Of course you still have to separate in Photoshop which may be more work than just printing in 4 color process in the first place. The benefit of process versus spot is that you don't have to deal with creating vectors, separating, overprints, color shifting from overprints, or chokes and spreads because the fills are percentages and one color touching another usually blends without leaving the knockout gaps one has to deal with in spot color printing. You do have to learn halftones, LPI and color profile selection along with some basic color management.
But that's why those who master these things make the big bucks. :ROFLMAO: