In the good old day of Feb-2012, aka Lightroom 1, Lightroom 2 or Lightroom 3, you could flag or rate a photo without worrying. With LR4, a photo can only belong to one collection! In LR1, LR2 or LR3, a photo can belong to many “regular” collections, with just drag and drop. Then you could decide on ratings or flags. For example, one photo can go in a customer collection and be rated as a 5 star, the best for that customer. I like that photo and want to add it also to my portfolio collection. In my portfolio collection, it should be only a 3 stars. I have much better photos than that, but that photo should be in the portfolio collection and if I find a better idea of what to do with it, it could even go up to 4 or 5 stars. Can't do that now anymore in Lightroom 4.
In Lightroom 1, Lightroom 2 or Lightroom 3, all the flags, pick…, and the ratings were local to the collection. Now in Lightroom 4, all the flags and the ratings are global to the whole catalog.