Its not so confusing while one is the vassal of the other one. But has anybody seen an AI colony break away from its master?
I remember reading somewhere that the colonies only break away if you treat them poorly. However, you already have access to all your colony's resources despite the fact they are a separate vassal, so there is no reason to be all pushy and demand stuff from them to make them angry. As far as I know, the AI always avoids angering their colonies.