Well, it appears you can choose the transparency for different sprites; the overworld sprites from Pokemon have the lightest shade in them, and instead use the second-to-darkest for transparency (it's hard to tell because the palette for that sheet is off so it might use the second-to-lightest, doesn't matter though). The actual background colour for the game may still have been white (all games have a standard solid background), but you can't tell that in the overworld because there are sprites covering it.
So, if you'd rather prefer to have the background be the darkest shade when making four-colour sprites, you could do that and use the darkest shade as transparency. It doesn't have to be the lightest shade.
EDIT:
Those sprites only have three colours because they're usually viewed on top of other sprites. Here they're viewed on a white background, but the white seen here is actual white and another colour is being used as transparency.
So, if you'd rather prefer to have the background be the darkest shade when making four-colour sprites, you could do that and use the darkest shade as transparency. It doesn't have to be the lightest shade.
EDIT:
(08-14-2014, 08:40 PM)jiyako Wrote: I decided to see how it would look in Nintendo's early style (pre-PKMN). I went with the Master System sprites 'cause Nintendo loved using big sprites. There are only three colors...
Those sprites only have three colours because they're usually viewed on top of other sprites. Here they're viewed on a white background, but the white seen here is actual white and another colour is being used as transparency.