You should always work with layers and they should have the same names and order, so that no problems appear with copy and paste and the setting in the layer panel 'Paste remember layers'. I recommend background, images, text, page numbers, logo down up. Put your logo on the logo layer on the parent page, background colors and background images on the background layer.
The problem is that any object on the pages will be above and covering all objects on the same layer on the parent pages. The solution is to work with layers. An object on the top layer will always cover objects on layers below, regardless if they are on the master/parent or on a page.
The other problem is, when you copy an object from a file with a layer and the setting 'Paste remembee layers' is active, the object is pasted on the layer with the same name and if such a layer is not found, it will be addes. And if the order is different, the visibility will be different depending on on the order of layers.
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