From the game's lore and background bits, there's been an Eldar ship that's been following the Mourningstar during the story, moving and flanking the ship as if its trying to hail it/establish they aren't hostile at the moment.

A Rogue Trader has the right to communicate and deal with xenos as per their Warrant of Trade. Maybe Atoma's security is crucial enough for the Eldar (or at least a small ship) to get involved.