All existing internet platforms already sit on top of protocols, the internet's running on them. Anyone can built a platform on top of ActivityPub, on whatever crypto network or what have you.
The old internet consisted of smaller islands not because of protocol technology, but because it had a small userbase overall and discovery was bad. The benefits of aggregation hadn't kicked in. If Mastodon gets to hundreds of millions of users I will bet that one or two instances will grow very large, develop their own rules, and what do you have then? A proprietary platform on top of what was once a 'first order' protocol. The protocol is still there but doesn't matter for end users, same way HTML doesn't to your average Facebook user or the blockchain doesn't matter to your average guy on coinbase.
People need to recognize that anything that increases connectivity between people tends towards agglomeration. Tech is inherently centralizing, even ironically enough the superficially decentralizing tools, if they lower the cost of communication. This isn't just the history of internet companies, it's the history of movement of peoples from fractured townships to large urban centers. It's not malicious platform lock-in, but simply gravity.