I think the MIB is quite sympathetic to some human being who might be the original from which the hosts are spawned from, and that the MIB is trying to help them escape. And that he communicated to Dolores in the barn and that whatever happened, it wasn't a rape.
What the Flick did a roundtable about the show, and one reviewer mentioned that all of these Easter eggs might be purely art set design issues and that all of that was clever and remarkable in the 1st season of True Detective, and intentionally or not fostered a huge conversation about the show, which then ended up being much less clever and somewhat straight forward at the finale. Sometimes people like puzzles and maybe this isn't the Gordian Knot.