First off big picture long term It would almost be nice to have a sortable "Shapes layer" list just for managing shapes in a layer naming them and the such maybe a shape manager or something to that effect where you can name reorder and change and see settings for shapes that are in the current active layer maybe even have liquid shape groups of some kind. I assume this would be a lot of work though...
On the more manageable side though....
1. Having a Liquid shape button to make a shape into a cutter so it always cuts through every shape regardless of where in the order it is.
Perhaps a check box for Cut all below and one for Cut all above so you could have it cut a hole regardless of its height in a stack
2. Have a check box on every shape that could make it immune to the cutter a lock of some kind.
3. If subtracting a shape from another making the Line where the cut happens inherit the line color or style applied to the subtractive shape. Might look something like this:
4. A button to make a shape immune to layer masking? Not sure if this would be possible but the fact we can change how each shape behaves makes me think about some past situations I found where I have a few shapes I want to be masked in the normal layer masking method where if I could have a single layer that mostly masked to the object underneath but I could just mark a few Shapes or Lines Lines to be immune to the mask and always render and not others that would be great. I know we can exclude strokes in full but being able to do so with segments or shapes as well I think would be useful perhaps.
Just a few early thoughts. Perhaps I will find other workarounds instead but curious what some folks might think.