I think that pwr connector has flat pins that require a slot, and last time I tried FZ couldn't do slots, at least not in the drill.txt file, so the parts has to have big holes because of the large pin widths.
If you are going to a PCB production house you can weave traces around so you could cut 3 jumpers.
You could also delete those 4 single header and connect directly, because currently that are sitting on the jumper ends not connected. It makes the SCH incorrect.
