Workaround: assign a http://docs.unity3d.com/Manual/LightmapParameters.html to the distant mesh and set pushoff to a higher value. This should take care of the floating point precision issues on faraway objects.

Cause: A high pushoff value means that the raytrace is started further from the surface of the objects. This can lead to artefacts if the pushoff is too high, caused by floating point inaccuracies. It will not slow down the bake.

Steps to reproduce:
1. Open attached project "790583.zip"
2. Open scene "test"
3. In hierarchy, select "Far" and notice that its position is (3000, 3000, 3000)
4. In lighting window, build lightmap
5. In hierarchy, double click on "Far" to focus on it
6. Notice artefacts

Note: Some artefacts are also visible when "Far" is as close as (500, 500, 500)

Reproduced with: 5.1.4f1, 5.2.4f1, 5.3.4p5, 5.4.0b16