>Assuming their input data is actually correct, I will speculate they are calculating the energy cost of the entire lithium battery production from raw materials, such as extracting lithium from mineral deposits, the majority of which would happen before the materials arrived at the Tesla factory.

If you look at one of their sources[1], it is clear that this is the case.

[1] http://www2.epa.gov/sites/production/files/2014-01/documents... p.65