Either way there's a chance things may go awry.I think if you cover your finished part with masking tape before you drill, that may be your best way. Is the contrast from the flat black dowels and the actual part that important? I think I'd stain the dowels black and finish the whole part, the dowels will still contrast. I'm assuming you're using the dowels as pins to hold the front to the main box and will be removable. Be careful, the dowels will swell and might pull out of the cover, glue them well.