The reason why a waiting tatkal clears cannot only be because of cancellation of confirmed tatkal tickets and rightly said by you that cancellation of confirm tatkal tickets seems illogical... There are various reasons... You can always have a instance where GNWL is all clear and there is still Bert's available from different quotas which enables confirmation ... Here we see a
#upgradation to 2 AC which suggests that the confirmation is due to seats vacant in 2AC and not because of cancellation of confirmed 3AC berths ..