There is exactly such a thing: it's called the assembly drawing output.
Usually this contains some mechanical layers which describe the centers or outlines of the components, the silkscreen (and therefore refdes, plus what the board visually looks like), and optionally, comments or other strings (as mentioned above) relating to footprint name, value/part number, etc.
I haven't seen a color coded / layer coded approach before. Most EDA tools have a fixed number of layers, so you can't keep adding one layer for each unique part on the board. If this were available, you could conceivably add a unique identifying layer to each unique component value in your library (so the schematic library would consist of e.g. one single resistor symbol, with hundreds of instances of values, part numbers and such; and the PCB library would be the same way, having one footprint and hundreds of instances of this customized layer or label property).
Finally, using such a tool: you could print a PDF version of the BOM, and add these graphical layers, which could be controlled with JavaScript; or the same thing in HTML in the browser. The layers themselves could be printed, physically, onto transparency sheets, but this wouldn't be very effective for BOMs over 20 or so (the transparencies simply aren't *that* transparent, enough that you can still see through a thick stack of them!). Or they can be printed onto plain paper, one or a few layers at a time, with a legend, which would probably be the best physical approach.
Not sure if that's quite related to what you had in mind, but it's an interesting thought to entertain. Maybe not the most useful compared to other tools or methods (like, a PnP machine
), but definitely within the realm of possibility in one of these EDA tools.
Tim