Excellent questions...and some very cool photos you have posted.
When I built my model of the Rufe that you have linked above, I really didn't know that much about WW2 Japanese aircraft paint and the various colors they used in general.
Tom Cleaver was 100 percent correct about bare aluminum metal and salt water. They don't get along too well. If you want to get rid of some magnesium, simply place it in salt water. It will disintegrate into nothing in no time flat... airplanes use magnesium in construction along with aluminum.
My understanding so far with the Rufe and the A6M-2 Zero is that they had a reddish colored primer paint over the bare aluminum. This red primer can be seen in this Zero photograph below.
If you look closely at this picture of a derelict Zero that is on display on top of a pole at Keita Memorial Park, in Papua New Guinea, it looks like there is some red primer starting break through the "Ame-Iro" top coat of paint, which has now faded to an almost white color.
"Ame-Iro" (or Caramel color) which is pretty close to WW2 German RLM 02, has been described by others as being very close to FS 16350, or FS 34201. These color conclusions were made using a Federal Standards book for comparison during the viewing relic parts of Japanese planes from the Pearl Harbor attack. Some of these parts were very well preserved and had not been exposed to sunlight too often.
I have a FS color book and used it during my Midway build on the "Koga" or "Akutan Zero".
http://imodeler.com/groups/75th-anniversary-battle-of-midway-group-build/forum/topic/tamiya-148-scale-mitsubishi-a6m2-zero-as-flown-by-petty-officer-1st-class-koga/
Here's a few pictures from my Federal standards paint color book showing the color chips that closely resemble "Ame-Iro". I wish the lighting was better to show the color more accurately. You can look at various pictures of my Koga Zero build here on the Midway Group build to see the colors in different lighting.
FS34201
FS16350
By Midway, many of the Japanese planes were over painted in darker greens on the upper surfaces.
This may be where the paint peeling comes into play. From what I can tell, the original Ame-Iro or Caramel color that these planes left the factory in was very durable. The problem with re painting is this:
If you don't have a proper preparation of the surface, (lightly sanding and making sure no oil of any kind is present) the top coat paint will not stick to the base very well. So during a wartime situation, I'm sure that the prep work was not as precise as it could have been under better environmental conditions.
I think that some of the paint peeling may have revealed the under color which was Ame-Iro and would have looked much lighter due to the color contrasts.
Later in the war, particularly the end, most Japanese planes were delivered in bare metal finishes and were camouflaged in the field. This is where you really start to see paint peeling come more prevalent.
Here's a color photo I found that shows derelict Japanese planes awaiting the scrap man just after the War had ended... Here again, there is a Zero in the foreground. This time it is a later model Zero, a dash 5 version. At this point in the war, shortages could have alleviated the use of some primer paints too.
In this picture of the A6M-5, the paint peeling has revealed something that looks like bare metal without primer underneath.
Hope this helps to answer some of your questions. I think this is an excellent thread by the way.
Maybe we can all add some of our research here ?