I joined a discussion on something similar on another thread. (Kicad-cli: export svg/pdf - no hole in THT pad - #12 by Paul.Blitz), but that was more about images for documentation rather than making PCBs.
Gerbers describe how the PCB is made: there is no hole, because the pcb process wants a solid pad, which then gets drilled and plated: the drilling information comes from the drill files.
So, looks like you may need to invest that time in doing something with those drill files.