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If you used the Pencil or Pen to make a closed path, it would then use the fill color that you assigned to it. I guess you must not draw closed paths when you use the Pencil tool?
But you don't have to assign a fill color. My personal choice for those tools, is a black, 1 px stroke, with no fill. But others might like to have a fill color. Who knows, maybe in their work, they only draw closed paths?