To answer my own question, it does appear that ue4 is smart enough to assign the correct lightmap channel to the newly created lightmap via the Destination Lightmap Index in that objects build settings. By default, this index is set to 1 for the second UV Channel. However, since One of my models was already using that slot, it automatically created the Lightmaps and set the destination index to 2.
It is the destination index that defines the lightmap channel address. Therefore, if you ever have a problem with your Lightmaps not showing up, check to make sure that your lightmap uv channel matches to the destination index. If not, switch the index.