External Lightmaps don't behave as internal lightmaps unity5

How do you setup external lightmaps in unity5? It's clearly not as simple as applying the maps to the lightmapsettings class. If I do this, unity gives me a whole world of weird behaviour.

Internal unity lightmaps that have been baked in unity seem to function differently to external lightmaps that have been brought in.
You will notice that the internal ones can go from completely dark to completely bright as you adjust ambient light and directional light settings.

External ones cannot go completely dark. They have a pre-defined brightness, and only go brighter than that.
I am baking externally and want to bring in the lightmaps, but can't replicate the functionality even when i
write a script to add the lightmap to the right lightmapsettings.lightmapindex

What am I doing wrong here? I've tried doing this with EXR maps and standard tga textures. I would like to use the internal lightmaps in unity5 as a guide, but can't even do that because they are contained in a snapshot which i can't access.

Do the devs have a link outlining this external process for applying lightmaps to models? Is there something specific in the advanced import settings that need to be set for this to work?