It's unclear how the DOJ got the keys to the guy's self custody if they were in his possession and he remains at large. Perhaps he had backups that the DOJ were able to access.
I doubt it's worth fussing over too much. 'Possession', in the legal sense, doesn't necessarily mean in your hands. It just means under your control. e.g. in the freezer of an apartment for which you are the lessee counts as in your possession whether you're there or not.
Interesting. Whether or not the DOJ has the private keys to the addresses listed in the indictment; it appears those addresses may be empty anyway.
For example, The first address (the only one I bothered to check) listed in the indictment at ~20K BTC has been near zero since 2020; and completely empty for over a year.
It sounds like they think they know that this guy was using these addresses; but, since the BTC has since been moved, they may not even know which, if any, of the BTC this guy necessarily still controls the keys for. Regardless, they are filing for forfeiture so that once convicted, he'll have pay it whether he has it or not.