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You still can get white background and colored buildings using a custom palette as "saturation" of a palette is determined only by its "light" color (i.e. the color of roofs). Example:

<svg width="90px" height="40px" xmlns="http://www.w3.org/2000/svg">
    <rect width="90" height="40"  id="paper" fill="#ffffff"/> <!-- White background -->
    <circle cx="20" cy="20" r="10" id="ink" fill="#000000"/>
    <circle cx="45" cy="20" r="10" id="medium" fill="#336699"/>
    <circle cx="70" cy="20" r="10" id="light" fill="#ffaa55"/>
</svg>
(+1)

 Hey Watabou, thanks for the reply!

Not too sure about SVGs or how to use custom code like you posted with the generator, I've been using export with PNG. Sorry to be such a total noob on the subject!

Like described here in "custom colors" section: create a new file, copy that code into this new file and save it. It's your "custom palette". Drag and drop it into the generator to update colors.