I might well give that a try Mik, my current favourite is to subtract the main model from the Subobject (in a different layer), move in really close and move the subobject about 1nm from the hull. With HTL, you can also get away with deleting the inwards facing polygons, not sure if this works normally though. But this still relies very heavily on the complexity of the surfaces you are joining.
One handy trick I've learned is keeping the UV Map open in one window, that way you can select individual points on the model from the Atlas map, which is a lot easier sometimes, especially when you are working on models with 'Internal' components.