Pete,
I think you are half right in your description of the process. Logically, the plate would be formed, the design layout done, the inlay completed, the sukashi, the plug for the ana, the design finished with the kebori work, the patina on the iron, and then for the brass. To cut out the sukashi and then inlay on top of it makes no sense, as it would over complicate the process. With brass being very, very difficult to gild in the fist place, it also makes sense that copper would have been used. It is much easier to gild if that was the desired effect. Also, we have been told that shinchu, brass was extremely valuable when it was introduced from China, so again, why not end with the copper? On top of that, gilding would be quite problematic due to possible overheating the other fine inlay.
I hope this helps clear, and not muddy the waters further.
Cheers,
Marcus