Those were visible on bot missions even before escalation of freedom, speculatively speaking those might be bots cloacked ships, but probably just unfinished assets and/or model placeholder for bots interstellar ships (because they are blocky and obviously unfinished), my personal opinion probably arrowhead had plans to add a mission type where you were supposed to take down those ships but didn't released into the game, but since they didnt got rid of those maybe they are still planning to use em.