Is there a way to tell it not to override this layer on certain layouts?
No there isn't. You can just use a different global layer.
Does that mean I need to be making every layout with the same number of layers, even if I don't need them on every layout?
This is not a good idea. If you want the global object to appear on a specific layer, the easiest solution is to create an event which will move it to that layer on start of any layout.