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.
Yeah, 'custody' can be a bit ambiguous. Furthermore, if the government indeed had control of the keys, why not simply transfer the funds away from still plausible control by the defendant?
"61. If any of the above-described forfeitable property, as a result of any act or omission of the defendant:
(a) cannot be located upon the exercise of due diligence;
(b) has been transferred or sold to, or deposited with, a third party;
(c) has been placed beyond the jurisdiction of the court;
(d) has been substantially diminished in value; or
(e) has been commingled with other property which cannot be divided
without difficulty; it is the intent of the United States, pursuant to Title 21, United States Code, Section 853(p), as incorporated by Title 18, United States Code, Section 982(b )(I), to seek forfeiture of any other property of the defendant up to the value of the forfeitable property described in this forfeiture allegation."
