You should really ask the print shop about how to set up your file. They should be able to send you a template of the punch form used and give you some guidance.
That said, a PDF can only ever be rectangular.
My guess would be that the print shop needs a file where the irregular shape touches the sides of the rectangle. The bleed is added all around the irregular shape.
The yellow area is your design, the cyan stroke is the document bounds and the magenta stroke is where the final print is punched.