The way anchor objects are implemented they are always in a layer above non-anchor objects. The use cases this was designed for are navigation, and notifications, which are typically on top of other content. We check and disable always on top to help indicate that these objects live in a layer above all other non-anchored objects.
We also thought about allowing for backgrounds where some anchor objects could be set to go behind, but this did not seem as important. What is the use case where you want anchored objects to be layered with non-anchored objects?