You'll never be able to do a proper job by using some filler and a spray can. In the majority of cases, people have had their complete boot lid re-done to blend in because trying to concentrate and blend one/two areas is "very" difficult. And... the time/money you'd spend getting somebody to do that, it'd be better to have the complete lid re-done.
Or... you go for the cheaper option and colour code your badges. That way... you only need to spend money on doing the badges and you wont have to worry about the holes left. So you have it subtle, effective and also cheap