Is there a way to have the new system overlay (using the constant combinators) but keeping the old 2x2 chest/overlay? I like using each corner for something with a different meaning. Usually I do:
•Top left - Machine that crafts things (e.g. assembler)
•Top right - Beacon (if used inside)
•Bottom left - Items crafted
•Bottom right - Modules used inside

An iron smelter would look like:
•Top left - Furnace
•Top right - Beacon
•Bottom left - Iron plate
•Bottom right - Speed 3 & Productivity 3 Modules

Sounds like a rather tricky user interface design problem. Maybe you have an idea how this could work and be used by the player, in a discoverable manner, such that overlays can be created with a choice between the old and new layouts?

What if instead of a single combinator being able to display the overlay on the full factory, you have 4 combinator, each being able to draw on a quarter?

That would just permit the old layout, but not the new layouts such as 1x1 or 2x3 grids.

What about adding a dummy item, that is an item that has no icon and shade? It would allow to create spaces in the overlay

That sounds like a fun idea!