1) What happened

In unity 3, when generating lightmaps, it would appropriately size them to 1024^2, 512^2, 1024x512, etc. In unity 4 it seems to be only 1024^2.

2) How can we reproduce it using the example you attached

Create a new scene and add a plane.
Click the Static box on the plane.
Go in lightmapping settings and set the resolution to 1.
Bake the lightmaps.
Notice that the plane is only using a tiny portion of the lightmap (under 'atlas'), but the lightmap is still 1024^2.