It's a good plan to get the code more documented, possibly it is a good idea to target interfaces between layers with some helpful Doxygen comments.
I see some issues down this line of thought however in that there are still many places where flashrom has half baked layers or plainly incorrectly situated ones such as programmer delay as the most recent example. Documenting may help reveal the truth but it can also solidify bad/incorrect code. Therefore it is worth keeping a flexible mind while broaching the documentation of each layer of if it is even actually correct.
One possible tactic to make some headway with this, rather large effort, is to divide and conquer it by having folks working on commits towards a specific subsystem/layer [sic. unit-tests, flashchips, programmer struct] follow up with commits that add some Doxygen comments at the boundary points of this layer/subsystem.
Another project is to ensure we expose this documentation in a up to date manner which fits into having a fresh, fun website that indexes the code comments so the documentation is actually well maintained and current.
Cheers,
Edward.