Holly carp, that must have been a bit of work.
Sometimes people use the PCB footprint to mount on custom boards, and there is a few tweaks you could do.
1 Could use a silkscreen outline in PCB. Silk is for superfluous stuff and should be above copper in XML.
2 The pins on the inside are actually there and will be drilled, is that what you want. Move them to silkscreen group for no drill
3 The copper layer is only on the top side so no tracks on the underside of the PCB can connect to it. Rename your copper group copper0 and put it inside a group called copper1.