They just straight up ram me while they are scanning me taking bars out of my shield.. Why?
So, to actually answer the question from a technical perspective, it is an issue of models vs game mechanics.
In the game mechanics, the ship is represented as a coordinate within the instance, more or less a dot on the map. When an NPC comes to scan you, they are coming to the dot.
The problem is, at the combat level, your model defines where you can get hit. So, navigation is aiming for a dot that is somewhere in the middle of the ship, while environment says that your 'Conda and their Viper cannot occupy the same space.
The solution would be to move their stopping point to about 1,200 meters so that they always stop outside the model. Presumably, the reason this hasn't been implemented is that the programming wasn't written modularly, so it has to be chased down each place that the logic exists in the game.