I know this might sound like a lazy answer, but that's the reason why I always clear coat. I've tried not clearcoating and got "exposed" edges as results.
Maybe to fix your problem, you could mask the area around the flaw. But around the edges of the target area lift the tapes a bit so some overspray can get through. That way when you spray you will get soft parting line between the new and old layers. Just dont put too much paint. Spraying wet clearcoat after that might flatten things out.