I've never used the plugin with that unchecked. Some tests suggest to me that if you uncheck that box, only the CP's with weighting percentages will be affected on the target model. Anything weighted 100 percent to one bone wouldn't be changed in that case. If you check the box, all of the CP's will be assigned even if the are weighted to only one bone. At least that's what I'm getting.
Hope that helps, Robert.