> Stripe also offers high-volume clients a discount on the 2.9% rate, which Patreon must be big enough to get.

Yep. They pay 1.9% (source: https://patreon.zendesk.com/hc/en-us/articles/204606125-How-...)

Also, Paypal offers a 5 cents + 5% micropayments rate that they take advantage of.

The 35 cents plus 2.9% is clearly designed to make you think that they are processing fees and I'd be very surprised if Patreon wasn't putting at least half of that into their pocket.