Each render engine procedural takes care of transferring the agent metadatas onto the render meshes, this process adds an "atoms_" prefix to all names. You can use these metadatas inside shaders to have better control over your agent variations at render time.
For instance, you can create an agent group with an addMetadata module. In the addMetadata options you set "myColor" as name for your metadata, the type to "vector" and then open the the agent override dialog to set random values on your agents.
Create a simple renderman pxrsurface shader and connect a pxrattribute node to the diffuse color. Set the "variable name" attribute to "atoms_myColor" and the type to vector.
Now you can export this material using the Renderman material exporter from the Atoms menu (or you can set up your variations scene and let the variation builder take care of exporting the materials).
Create an agent group and set the variations on your agents. Once you will render, you will see a render similar to the picture on the right, where the shader color is taken from the myColor metadata.
This can be done also in Arnold using the aiUserDataVector/Int/Float/... node or in V-Ray using a VrayUserColor node.