The general consensus is that the EPA is indeed basing MPGe on "wall to wheel" energy usage, in controlled conditions. This is what I recall reading in multiple places. Spending a few minutes on this, I'm not finding much corroboration in official documents, but the numbers do add up as discussed above.I would be very curious to see your reference for this, as charging losses are variable depending on the items I noted above.
Here's an older TM forum thread that addresses this:
Model S EPA rating 89 MPGe | Forums | Tesla Motors
Take it with a grain of salt, but this Wikipedia entry can be a good starting point, and it does state that "wall to wheels" numbers are used:
Miles per gallon gasoline equivalent - Wikipedia, the free encyclopedia
Also, one big negative for gasoline vehicles in the cold is the need to run the engine "rich" for a longer period of time. Not only does this use more fuel, it produces more fumes. Cleaning snow off of a warming-up EV is so much nicer for this reason.