In legal terminology, custody in this context is the government's claim over the asset regardless of actual possession of the private keys. You can see in the court document that the Bitcoin is in "addresses known to the government" and the DOJ "requests that: warrants be issued..." and "due process issue to enforce the forfeiture of the Defendant Cryprocurrency". There is no evidence that I can see (yet?) that the government has actual control of these funds.