I notice that the colors in Simulink look different from colors set from MATLAB. As an example, if you right click on a Simulink block, and select "Background color -> Yellow", you will see a different shade of yellow than if you executed
figure('Color','yellow','MenuBar','none','Name','Color','NumberTitle','off','Units','normalized','Position',[.2 .8 .3 .1])
It appears that MATLAB and Simulink do use different palettes. MATLAB appears to use 'pure colors', for example Red corresponds to an RGB triplet of [1 0 0], just as you would get from many programming environments. Simulink appears to use a more subdued color palette, where for example Red is [0.9 0 0].
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