The writers aren't completely "sovereign" as long as they are using Stripe (and Visa and Mastercard) to process payments. It is basically inevitable that some entity in the payment system will eventually interfere with Substack even if Substack themselves hold the line.
True, but messing with people like Greenwald, Tufekci, Taibbi, Yglesias, Sullivan etc. at the same time is bound to get Stripe into a world of hurt. These are names with a following and they have strong incentive to stick together if anyone on Substack is threatened with financial cancellation.
It is unlikely we will ever even hear about Stripe openly leveraging their influence. They will talk to Substack, who will bring the issue to their investors, who will tell Substack that Stripe is higher up in the food chain than the writers.