As I said, there is 100% logic in the holes on that plot being filled in, as I believe “plotting” is used to create the details for manufacture, I guess exporting does the same.
Ok, another idea for you: have you tried to PRINT the PCB (print to the Microsoft / other PDF printer)? If you print the copper layers, there’s holes in the pads! Like this:
To make that image I did a print in colour, then set my printer to be the PDF printer: looks good to me. Just select which layers you want - make sure to select the “Drill Marks” to be “Real Drill” . You may need to have a play to get what you want. If you select “Black & white” then you end up with a lot of black on top of black 
Ok, how about his (may need a bit of playing), but in Print, I selected the F.Silkscreen, F.Fab and the edge cuts, and went with B&W:
(for some odd reason, my component values, which SHOULD be in my F.Silkscreen layer, don’t show up if I just select the F.Silkscreen layer!! Version 6.x)
(the Print function has a very useful “preview” option, so you can quickly see the effects of selecting different layers, colour vs B&W etc…)
Another possibility might be to select your desired layers in Kicad (in “appearance” menus) then do an image grab? With custom colours, might give you something usable?
If YOU don’t find this comment helpful, then dump any flames in the (fireproof) bin, I’m just trying to help you and others…