Here is a helpful tip from Jed Smith, who shows how you can use the output from a RotoPaint node in Nuke to separate the results from the background. The idea is that you can use the isolated strokes from the RotoPaint node for warp, morph and color correction tasks that will ultimately make the painting integrate better.
There is also a little walk through of the benefits of linking roto and transforms to tracker nodes in Nuke. Jed does mention that the techniques that are covered here, may not be suitable for all situations.
There are times where it would just be easier to paint a clean plate on a single frame and track that in, rather than only using the strokes that generated the clean plate. This strategy is very useful in many circumstances however, especially when you need to extract only the area affected by your paint.