The proper handling of fifty-two flags was known at the outset to be a difficult task. They are raised and stored automatically from recesses in the poles themselves. The original plan called for each pole to have its own light and moisture sensor, though I have a hard time believing the equipment would have held up through nearly twenty years in the weather. 3D two masts. I think that's the British system, too.
Every flag is intended to have it's own.
In most places they are flown at the same height. Maybe a result of the lot of independent German states, kingdoms and cites in German history. If an flag pole is higher, it's always in the middle of the display for the main flag. The highest flag has to be in the center. If their are more flags, they will be added on both sides.