When you pose your base armature and generate the rig, it populates the controls and the "green bones" that control them in hidden layers. Now, is it okay to move these green bones to move the controllers for the rig in more fitting areas for the mesh? It's a lot easier than undoing the rig, editing the base mesh, and generating the rig over and over again but I'm not sure if this will cause problems later on.

And side question, why are the bones in these layers green while others are the regular gray color?


Green means the bone has some sort of constraint on it, so other bones can interact with it. This is useful because it means the animator does not need to animate every single bone and instead just animate a few main bones.

You can always move the green bones, just make sure you are in Edit Mode. You might not be able to transform them in pose mode because it might conflict with the constraints.

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