It seems that will depend on their payment processor and the bargaining power of Patreon. If no processor wants to lower their charges there is not much Patreon can do. Similarly, if Patreon are not a big ticket fees generating customer they don't have much leverage.
How to do a profitable micro transaction is still a mystery.
It shouldn't depend on the payment processor; if the credit card payment is going to Patreon, they can batch up the charges however they way (e.g. they could batch up all of one customer's donations for a week to 50 different artists, and process a single transaction with their payment processor for the whole amount. They would then only be charged for a single transaction)
Even if it was 1:1, actually charging the payment processing fee for the payment processed would be fine. The person with one pledge for $1 to one creator would be charged $1.38. The person with one pledge for $100 to one creator would be charged $103.80. The person with 100 pledges for $1 to 100 creators would be charged $103.80. Fine. With the rules they're putting into place, the person with 100 pledges for $1 to 100 creators will be charged $138.00 - with the other $37 going to Patreon. Not cool.
How to do a profitable micro transaction is still a mystery.