In response to some understandable confusion over this aspect of Mitsubishi Zero factory paint colour here are schematic models to help demonstrate the paint degradation explained on page 11 of the e-guide.
The top gradient shows the typical "average" oxidisation and chalking of the exposed paint surface as it is affected by the environment, shifting from a glossy amber grey to a dull, flat dove grey in appearance. The harsher the exposure the more rapid the shift and in some cases beyond the dull grey shown at the end of the gradient. This gradient represents the typical "journey" of the paint on an aircraft as it might be represented on a model. Diligent maintenance of the paint surface would reduce and delay the shift but not eradicate it entirely.
The lower gradient shows the typical thermal ageing of paint protected from light and exposure for many years (such as the paint layers beneath the oxidised and chalked top surface or preserved paint samples). Again dependent upon the storage methods and ambient temperatures, etc., the darkening and browning of the paint can go beyond the extreme end of the gradient or result in a variegated appearance on the paint surface.
Variegation in the paint surface can also be induced by localised extremes of heat such as around the engine exhausts and also by the affect of solvents such as fuel or oil.
Whilst the contrast between upper and lower extremes may seem harsh note that the incremental changes in each direction from the original paint are relatively small and subtle. Bear in mind also that Nakajima paint was often more amber yellow in appearance to begin with.
Image credit: Schematic model © 2011 Straggler