To answer the “why” on two colors of Pandemic Legacy:

The game is played in a series, almost like a campaign, over 12-24 sessions. The board changes permanently, and story/character events take place in each session. Once you’ve completed the campaign, the game isn’t really replayable.

The two versions are differently-colored so that you can be playing through two campaigns concurrently with different groups of people, and easily keep the two boxes separate.

Or, just for prettiness.