I can only guess that it's to avoid multiple entries with the same "popular" numbers. The chance of any one combination winning is the same. However, the payout you get when winning a popular number may be less because it may be shared with others who also played that number.
By adding a few randomly generated digits, the chances of two entries based on the same popular number ending up the same are decreased. For example, if two people play the same popular number but the system automatically adds 3 random digits to each, then there is only a 1 in 1000 chance the two entries will be the same, wherease there would be a 1 in 1 chance they would be the same otherwise. The odds of winning are the same in either case, but the expected value is only slightly decreased by the other player when random numbers are added, whereas it is halved without the extra random numbers.