I don't think anyone would mind if you edited the model to have a custom bracket or strut to brace the docking point. After all they did say in the mission that they had to reinforce it. This would give you enough of a gap that there wouldn't be an intersection between the models.
And, for aesthetics sake, could you flip the assembly over, so the Chronos is 'right side up' and the Cain is 'upside down'? I know that's how they're oriented in the mission, but it just feels better that way... and there's no 'up' in space anyway, only the camera orientation.
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