Michael, I'm not sure I understand your point correctly, but the calculations do take into account the production of the fuel. For example, only 80% of carbon emissions associated with burning gasoline comes from the tailpipe. The remaining 20% is accounted for considering extraction, de-sulfurization, refinement, transportation, etc.
The GREET software also takes into account the well/mine-to-outlet emissions of power plants.
As SByer said we could die on the details. For example, people working at a nuclear power plant still have to drive to work, which causes emissions, but they would probably be driving to work anyway if they weren't employed there. Car makers use energy to make ICE vehicles, but also to make hybrid or electric vehicles. In that sense, it's all a wash. We could quibble with the numbers, but I doubt it would change the conclusions much.
What I clearly convinced myself of is that driving a modern, electric vehicle is not a "long tailpipe" that's worse than an ordinary ICE. In most real world scenarios the pollution is reduced. Not so with coal, compared to a Prius, at least in a very obvious way, but it's still much better than an ordinary car.
The real beauty of EV's is the dovetailing effect it can have. People buy zero or low emission EV's, behind the scenes the power plants continue to clean up over time via regulation, now oil is no longer a strategic commodity but a mere commodity and we don't care where it comes from or how much it costs, traffic is quieter, there are fewer toxic emissions around population centers, less smog, etc. EV/PHEV's really are a no brainer with zero tradeoffs (except for initial cost! but that will change).