Re: A few pertinent questions....
They are actually making more money out of the deal. On the App Store they get charged $3 on a $10 purchase. If you buy direct then they charge you $8 for the same thing, so unless their transaction cost is more than $0.99 (unlikely, CC companies charge circa 2-3%) they get more in their pocket.
Meanwhile Apple also support purchases by gift card (so they need to give stores a cut), customer refunds (remember the scandal when kids were purchasing using their parents linked credit cards) and curation. It's not all gravy like Epic seem to claim.