That depends on their merchant account. For example, Square offers an "unlimited" account that charges one flat fee for up to a certain dollar amount (varies based on how much you pay per month) with no per transaction charge. There are others that charge say 1% of the transaction as long as it is over a certain dollar amount ($100 would always meet this), again no per transaction fee. These deals are only available to larger companies that do a certain minimum volume of charges and I can't imagine a business as large as Disney doesn't hit that minimum to qualify for these deals nor can I imagine that they are paying a per transaction fee.
So, I seriously doubt the extra charges would cost Disney anything and if somehow they are getting charged per transaction fees, every $100 would be better than people using the cards in the parks for every $5 charge and such.
Also, if they changed to charging every night (at 2 AM local time) or every $100, whichever comes first, it would bring their system even more in line with how the
Disneyland Resort Hotels handle room charges and have a unifying system where no matter which coast you were on you would know how room charges work.