Just researching for a different game I want to make, and stumbled across this which may explain some things?
"For dozens of popular Game Boy titles, the Game Boy Color has an enhanced palette built in featuring up to 16 colors - four colors for each of the Game Boy's four layers. If the system does not have a palette stored for a game, it defaults to a palette of green, blue, salmon, black, and white. However, when the user turns on the system, they may choose one of 12 built-in color palettes by pressing certain button combinations (namely a direction key and optionally A or B) while the Game Boy logo is present on the screen."
On the Gameboy Advance page, they also say this: "Game Boy games can be played using the same selectable color palettes as on the Game Boy Color."