base-palette's current grammar is:
base-palette: <integer> | <string>
It's currently impossible to tweak the colors in the "dark" palette, because base-palette can't identify the dark palette - it can only identify palettes by their individual indices or localized name.
So, just like font-palette has:
font-palette: none | normal | light | dark | <palette-identifier>
base-palette probably should have:
base-palette: light | dark | <integer> | <string>