Not sure if this was 'pinball savvy' - but I did this once a long time back.
I drilled it out with a slightly larger bit than the hole itself so after the drilling the 'mound' was reduced a bit as well - I then used a 'conical' hard sanding bit in my dremel tool and turned it into a smooth edged crater , rather than a volcano. Then I filled it , sanded and re-painted the small section.
Not sure if there is a way to do it AND minimise the damage/ area that needs to be touched up after
