I have made these changes in my own Prusa Slicer configuration, and it working quite well. I can use whatever filament I want, and the machine section takes care of the tool change gcode. The last issue I am facing is a long-standing bug in prusa slicer where it fails to emit an M106 for the second extruder. Can be fixed by setting to a constant speed, but that doesnt compare to Prusa Slicers auto fan speed stuff.
Overall I would say Prusa Slicer is not particularly well suited to multi-extruder machines at the moment. For example, the prime tower is a single volume for all materials, which will cause problems when one of the materials is designed to not bond so well (such as breakaway support material). Cura solves this by only priming each material onto itself. I expect this to get better with the eventual release of the Prusa XL.