About Creating Layers for Subtractive Features
Subtractive features (cuts, holes, and so forth) in an assembly must be created on intersected models. A new layer is created if this condition is met, and the default layer is defined in the configuration option.
When you create a subtractive feature, the visibility of the feature must be set to a level other than the top level. For example, in assembly A with parts B and C, if you create a hole in assembly A that goes through part B, you must go to the intersection section and specify that the cut be visible at the B part level. This action adds the feature as an assembly cut to part B, and a default layer is created in part B.