If I'm not mistaken, the refillable mugs at the water parks are one-day use, right?
If there is a problem with the barcode, it is fairly simple to deal with it since it had been purchased at the location earlier - you should still have proof of payment, and only a day of records needs to be checked.
With the resort mugs, they are good for a much longer period. Problems with the barcodes can result in long lines at the register, lost proof of payment requiring long lookups, etc.
Now, I could see them adding a new entitlement type to a KTTW card, for a refillable mug purchase. Just call it "unlimited drinks", guest can use their own (reasonably sized) cup or purchase a souvenir cup, and a card reader at the dispenser. But I can also see longer lines at the dispensers since it will take time for each person to use, etc. whereas right now several people can use the same dispenser at once.