Problem solved. If anyone else runs into this, this is what I found works:
Apparently, the auto silk generator only recognizes lines, arcs, and text. It does not recognize shapes. Before, I was only putting MANUFACTURING/AUTOSILK_TOP on my silk screen artwork file. If I add PACKAGE GEOMETRY/SILKSCREEN_TOP, which has the pin 1 designating circles, they also appear in the artwork.
Interestingly, in the more complex example I mentioned above, somehow, when I imported the dxf file, it must have put "lines" all around my custom ESD symbol. Then, the auto silk generator recognized the outline, and put it in the AUTOSILK_TOP layer. However, it did not recognize the fill. If I add the BOARD GEOMETRY/SILKSCREEN_TOP layer (which has the symbol, fill and all), I get a filled shape in the artwork.