Yeah, the factory clear was sanded on the whole car, and then the stripes were painted. Then the car was re-cleared and wet sanded. Cost me $2500.
You can paint your stripes right ontop of your current paintjob though. I believe the stripes get masked off, then the clear gets skuffed, then your stripes get painted. I believe that's how the factory stripes get put on.
The difference is that you can feel a slight edge on the factory stripes. On mine, they are smooth. Up to you wether you think not having some thickness on the stripes is work the extra money.