Keep in mind, Defend started out as defend a location in space, not a ship. So I'm pretty sure when Alex updated it to be able to placed on ships, he didn't change any of the internal logic or flags or what have you. I'm pretty sure defending ships have no concept of a ship at the defend point, but are just treating it as a point in space around which to fight. The usual local AI then fights as normal, with some preference to be near the defend point.
If I think back to when I've got a frigate with a defend order at a capture point, and an enemy cruiser comes up, that frigate backs off because it feels out matched. That same type of behavior is going to happen when defending an Atlas. If there's a friendly cruiser behind the frigate a ways, it might back off until closer to the friendly cruiser, and then might try to start to flank depending on circumstances. Or it might just keep backing off in a different direction and just drag the cruiser away. Since the Atlas is a capital, it's going to tend to feel more confident in engaging larger enemies, or massed enemies than say frigates and cruisers and will naturally come to the front on an engagement line.
Escort clearly has a concept of the ship, as they keep to specific orientation, typically to the flanks or rear to prevent flankers. They also tend to keep much closer than a defend order. This is presumably to keep the front where most ships have more guns, clear for shooting. Also, the AI doesn't like getting flanked and will waste time turning if there's friendly ship in between it and a closer enemy to the rear, which an escort frigate is pretty good at doing.
If I want a ship to be behind the main line, I give it an escort order to an Onslaught or Paragon. I'll often order carriers to escort Onslaughts for example, and they'll tend to do a better job of staying out of direct fire (not always, as escort logic tries to move to the front if the ship is overloaded). Of course, that doesn't typically help a primarily direct fire ship like an Atlas, or if the Atlas is the biggest and slowest ship you have.