If you trust the judgment of the (admins of the) sites you are syncing with, this isn’t a problem. If you don’t trust that, don’t sync with them.
For instance, if I wanted to run my own server, I would absolutely sync with lemmy.world’s block list. I agree with their stated defederation policy, and have seen no evidence of the admins disregarding it.
Perhaps you are misunderstanding what this tool does?