It doesn't prevent them, but with IPv6 everyone can take back control. With IPv4, you are unable to get a decent amount of public addresses to run your service (if you are not having tons of money already).
You are talking about lower layer protocols here that don't matter for decentralization. In fact, a decentralized transport protocol can be made that doesn't require your ISP to give you an internet routable IP address nor put you behind NAT.
Think e-mail, for example. It never required you to have an internet routable IP addresses to communicate with anyone. There were and are plenty of local networks where people run local SMTP servers that communicate with upstream SMTP servers over local network and only those have public IP addresses to communicate with SMTP servers over public internet.
Any service provider can just decide not to route consumer-facing IPv6 addresses. It's not like we all had tons of our own free routable static IPv4 addresses two decades ago, you still had to get them allocated from a service provider and have them route to you, and be allowed to host services. They're "giving away" IPv6 routing and allocation right now, but there is absolutely nothing stopping them from ending that practice.
Think e-mail, for example. It never required you to have an internet routable IP addresses to communicate with anyone. There were and are plenty of local networks where people run local SMTP servers that communicate with upstream SMTP servers over local network and only those have public IP addresses to communicate with SMTP servers over public internet.