Actually, I do know two ways to combat this issue, here are the choices/options I would suggest:
Make semi-transparent layers between the object level layers by generating a white color in the color palette at around 80 alpha and filling in that layer as a semi-transparent background, or a sheet of tracing paper layer if you will. For the layout backgrounds, sketch them in a drawing program like GIMP, set the opacity to around 33%, export them as transparent .PNG files and import them into Pencil2D.
Make object level layers with the semi-transparent white backgrounds within them and draw over them with the pencil tool in black, eliminating the cumbersome semi-transparent white background layers between them. If you have to erase something, paint the colors black and 80 alpha white outside of the camera and background area. Use the eyedropper tool to extract the 80 alpha white color and “erase” the unwanted drawings with the pencil tool, then use the eyedropper tool again to extract the black color to resume drawing. Repeat as needed. The layout backrounds I’ve described in choice 1 are to be left alone because they are already semi-transparent as they need to be.
I hope one of these options work for you, but I would recommend choice 2 for efficiency reasons.