So basically, the color parameter the cutscene editor changes is a property of the material. I.e. all objects / sprites using this material will automatically be affected as the material is shared between them. if you want to then change 2 sprites independently using material parameters, they will need unique copies. (which will break all forms of batching too, and performance will suffer, a lot)
Thats why the 2D Toolkit sprites use vertex colors to store color / alpha per sprite. That way you still share the material, but change the alpha property in the mesh (indirectly, through the accessors).
I'm not sure what would be best to recommend for shaders within Unity. The combiner syntax which the 2D Toolkit shaders use is specific to Unity - this is intentional to support older devices and hardware.
If you want to learn about hlsl/glsl/cg there are TONS of tutorials online - they will all be very relevant to how the cg shaders work in Unity.