This post started as a Hacker News comment.
The biggest immediate danger for writers of Substack's centralization is that they've introduced some subtle lock-in with their reader app. Substack is quick to say that you can always export your email list and move to a different newsletter provider. But if your readers have built a habit of reading things in the Substack app instead of their email inbox, then moving your email list somewhere else means your readers will be less likely to engage with your newsletter. They will have to make a behavioral change. Some readers will make the change and go back to reading your newsletter in their inbox, but some will just go inactive instead.
If Substack actually cares about preserving writers' independence, they should provide a way for writers who switch platforms to continue delivering their newsletters to the app. For example, they could give app users an @inbox.substack.com (or whatever) address. Anything sent to that address will show up in the app. When you export your list of Substack subscribers, you get both their regular address and the @inbox.substack.com address, so you can continue delivering to both their email inbox and the Substack app.
Until Substack does that, I'll continue to view their claims of putting writers in charge with a measure of wariness. I do think Substack/Substack's founders are sincere, actually. I don't think they're twirling their mustaches, thinking "How can we lock people into our platform?" They're just way too confident in the righteousness of their cause, and as a result I don't think they look inward enough in situations where the interests of Substack, writers, and readers conflict.
(And no, using a paid subscription model instead of ads doesn't magically make all incentive alignment problems go away.)
 For example. When the app was launched, by default they stopped sending emails to people who installed the app, which would hasten the inbox->Substack app behavioral shift I discussed above, strengthening lock-in. They switched it to opt-in after backlash from writers.