Yes extra holes have to be in the copper group or they don't get drilled.
Yes they are duplicated because when I used the FET to make the part I modernised it with the non duplicated method of nodes in copper0 inside a empty copper1, and the drawing came out as above. I also got the error that FZ can't do separate copper layers even though they were inside each other. I basically mod-ed the working V-reg part the minimum amount - i didn't want to break it like I broke the FET -, so there would be no faults.