To get around this, I xreference the base drawing and change its name in the Xref Manager by typing (in this case) the word Power in the Reference Name field.
Then I Xreference the base drawing again and rename this second version to Lighting. The effect is the one base drawing has been referenced twice but with different names resulting in separate layer names.
This gives me separate layer control of each.
Your case may not be lighting and power, that's okay, because it will work for what ever you need.