It undercuts Epic's case in two ways. First it greatly weakens their "we're all in this together" approach with other developers. It was always a dubious alliance as the companies in it have different goals, and Apple's move divides them further. I think many small developers will be happy to pay 15%, and few share Epic's attitude that they should pay Apple nothing.
Second it makes it clear there's no economic justification for Apple's fees. Economically it would make more sense to give large developers a discount, as they pay more but don't cost a lot more to support. But charging large developers more makes it clear that Apple are doing it as they can, as those companies can afford it.
This may seem perverse, but it's the approach Epic take with Unreal engine. It's the approach Harman take with the AIR SDK. It's common in tech, to charge your large customers more and have cheap/free tiers for small customers (who might one day become large customers). It's hardly fair of Apple to arbitrarily set a $1m limit. But as it's common, and as Epic do exactly the same, it will hard for Epic to argue against it.