There are people who think that the GenSurg guys will somehow find out that you also applied to their PRS program. They might.
The bigger issue is strategic applications. When I applied to GenSurg, I didn't apply to any programs that had INTEGRATED Plastics residencies. My opinion (based on what I saw at my school and my away) was that GenSurg residents at a program with Integrated Plastics won't get the same interest from the Plastics faculty because they're preoccupied with their own residents. Conversely, I made sure that every GenSurg application was to a place that had a Traditional/Independent Plastics program.
Fortunately, I matched Plastics, so the point was moot. (Good thing, too, I hate GenSurg and wouldn't have made it through).
Maximize your chances to match:
1. Get great letters from known PRS Chairmen/PDs
2. Rotate at at least one program besides your home institution
3. Apply broadly. I applied to every program except for the ones in NYC and LA. I just couldn't see myself being happy living in those two cities for six or seven years.