@hkz i've had success with this being done correctly by putting the holes in…

@hkz i’ve had success with this being done correctly by putting the holes in the NPTH drill file and having a drawing layer with a callout pointing to each hole and specifying “NO PLATE!” and then putting the same thing in the job comments.

BTW the holes exist on the original because the board was etched first and then electroplated with gold, so the traces are all electrically tied together. afterwards, the board is drilled to isolate the nets.