you can pass for example colors by using vecDiffuse, vecAmbient, vecSpecular and vecEmissive
if i got your question right.

however i think that what u do in a shader is generally what will get rendered. for example if u write a fixed color value using def c0,1,0,0,1 and mov r0,c1 you will get a plane red no shading no nothing else, doesnt matter what else is done in the material settings. of course if u use AlphaBlendEnable and BlendOp you can manipulate the way this plane red is mixed into the scene

the difference to other fx-files is that 3dgs uses not all features i think, and the engine structure is built in a own way, so that the fx-files will have to look so, too