Edith,
You are correct in what you have found out about the encouragement of certain rules for winter camping in the BWCA. The US Forest Service encourages people not to camp in designated campsites and to make fires on the snow. This is to provide a rest period for the campsites to have a chance to recover for the next season, for what it's worth. They do not restrict camping in a campsite though, as that campsite might be the only opening in the forest big enough to set up a shelter. Check out Page 7 of this PDF:
US Forest Service Boundary Waters Travel Personally, I avoid camping in designated campsites during the winter. There is usually enough snow on the lakes that setting up in a nice protected cove is ideal. Also, wood gathering is much easier the further away from a summer designated campsites you can get.