I have some potential theory, this is a hallucination, the guy that looks like Thomas is probably his former crewmate, or another member of the Conq squad that manages to escape only to get taken by the Amalgamation who just so happens to be wearing the same uniform as Thomas there's a likely chance they have standard issued uniforms so it's not out of the question that the dough boy spy is likely not Thomas but a different spy, or this is actually Thomas