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I have found a fix: resolution in game must be on Native, otherwise the game's scaling system interferes with freesync.
If you need to game at a different resolution from native, select Native in Sea of Thieves, and change your windows desktop's resolution after the game has started.
Using ReLive and overlays in game can make freesync stop working again. To quickly fix without restarting the game, change resolution from Windows to something else, go to the game again, and change the resolution in Windows back to what you wanted.
It's a bit annoying but at least it's possible to make it work. Hopefully future updates will smooth out these issues.