In my research for that console, I learned that the RF connector of the japanese SCV really change the balance of colors. You can also use the RGB outs in japan, but if i understand correctly, few did. While in france (YENO brand console), _only_ the RBG signal was transmitted on the SCART connector, and its what im using.
Some people use modified eSCV emu with different color schemes if I understand correclty (its hard with approximate japanese->english translation).
Anyhow, the current colors in MESS match what I get on my french console with RGB outs. And the new colors in SVN come from voltmeter checks that i've done myself on the truncated scart output pins.