They were made that way because the new non-toxic primers have a different pressure curve than the older lead styphnate primers. When they tried using the NT primers with the smaller flash hole, the primers backed out. The original fix was to crimp the primers in, just like military primers. The latest fix by both Winchester and Federal is to enlarge the flash holes, which works.
Eventually, all their brass of current production will have the larger flash holes. Just load them as usual and don't worry about it, according to the technicians at both Federal and Winchester. I've been loading them alongside the older flash holes and I can't tell the difference when I shoot them.
Hope this helps.
Fred