I feel that among other things, it speaks about the delicate balance in the App Store that nobody is acknowledging.There are ways they could do it but they would require some form of invasiveness. However, charging a percentage isn't new or unusual, the MPEG group does it, so does Qualcomm, so does Unreal, etc... It isn't an unheard of practice.
I think the only reasonable way they can actually make the CTF work is some form of revenue percentage cap, otherwise there are always going to be apps with low per user revenue but high user counts that won't be viable under a static per download amount. (Unless the amount is so trivial as to be not worth implementing).
I think Apple knows that the CTF isn't a system that will lead to a healthy platform, and if applied to apps in their own store it would lead to many apps switching to PWAs, which I don't think Apple wants. This is why IMO that the changes they brought didn't bring the CTF to their own store and allowed devs to continue on with the existing terms.
You are right that free apps don't pay Apple a cent, and I don't think this is an oversight. For every Facebook or Instagram that generates billions for its parent company, there is a free app by some aspiring developer who is still in high school and just wanted to get an app out there to build up his portfolio and gain some experience (for example, I use a free app that displays my bus arrival timings). I don't think there is a feasible way that Apple can attempt to have their "pound of flesh" from Meta without having indie developers also caught in the crossfire (like how do you distinguish a free app from a multi-national bank vs one released by a kid in school?).
The intent here is really to keep the barrier to entry as low as possible to incentive as many people to release apps for iOS as possible.
Instead, it is the 30% from paid apps (more specifically, freemium games) which make up the bulk of App Store revenue and make it worthwhile for Apple to support all these free apps. Some may argue that it is unfair for a company like spotify to pay so much to Apple, and I would liken it to how people who earn more in a country tend to pay more tax (and the tax revenue then goes towards programmes which aid the poor). That Spotify has to pay so much to labels as well is a problem with their business model (who asked them to enter the market knowing it was unsustainable in the first place?), not with Apple.
Of course a developer who makes more money would want to keep as much of it for himself and pay Apple as little as possible. It's human nature. But would you then be okay with a millionaire not paying his fair share to government coffers using the same logic?
If you want a system where Epic gets to keep 100% of iAP revenue from Fortnite, then maybe one way Apple could make up the shortfall would be to increase the annual developer fee (maybe double or triple it across the board for starters). Again, barely a rounding error for a company like Facebook, but you just raised the bar of entry for new developers, and it's the vitality and vibrancy of the App Store (and consumers) who suffer ultimately.
I don't think the App Store should be a loss-making venture.
And seriously, is there anyone here who really cares that games like Genshin Impact or Candy Crush are keeping only 70% instead of 100%?