That is indeed the correct and desired behavior, because we do not want to futz with changing strength ordering of opinions by moving specs around between layers in the layerStack. So, each layer in the layerStack that has “before namespace” opinions, is updated to have “after namespace” within itself. Also, as the example at the top of the Namespace Editing user-guide describes even more simply, if you want to delete a prim, you need to do so from every layer in which it appears.
And just in case you were thinking maybe to see a “relocate” in the stronger layer… relocates can’t apply to specs in the local layerStack - only to prims/namespace coming in over composition arcs.