As a layout artist you see your project as a whole. Not as a collection of single pages. For the latter one better uses a illustration app like AD.
I consider it's a big mistake adopting the level concept of AD and AP for AP. Most layouters use layers primarily for alternative designs, which can then be faded in and out with a single mouse click. Exactly this is not possible with AP and its current layers concept.
I know, it is difficult to change, because AP should be compatible with AD. But maybe you could bypass the problem by offering the option to mark selected layers as cross-project. This could be a publisher-only function.