In my example the different geomerty is nested under a gameobject that acts as the pivot. This parent game object is used as the Unity_Mesh reference that feeds into the object merge node. I thought the merged geometry would use the transform location of the specified game object.
The plugin recursively finds the valid inputs of the gameObject that you input and then marshall data into Houdini one by one if they are valid. In this case, it will ignore your parent "pivot" gameObject. I'm not entirely sure if this will help, but have you tried playing around with the "Keep World Transform" or the "Pack Geometry Before Merging" options?