If you go through the Fuel Tank Tour, you'll find out that the fuel feed line from the tank begins at the base of the flower pot. In fact, it starts right from the drain plug/filter. In other words, the fuel in the flower pot and the fuel in the feed line are separated by the filter attached to the drain plug. So, if the black stuff only shows up when you open the drain plug, then the drain plug/filter is doing its job well!
When you siphoned fuel out, it probably came from outside the flower-pot. So, as you've noted, it would appear that the black sludge build-up is restricted to the flower-pot.
Be warned that there is a little hole at the base of the flower pot through which fuel enters the pot from the rest of the tank. In addition, the fuel return line goes straight back to the flower pot. These entry holes are relatively small and can easily get clogged.