If you move from a central hub and spoke electricity distribution to a decentralized model, that alone is a game changer. You don't need to worry about the grid at all.
1. 3.1% seems low. Another estimate from 1995 says 7.2% (http://en.wikipedia.org/wiki/Electric_power_transmission#Los...). I suspect that the truth is closer to 5%. Also, the losses incurred are dependent upon the distance. Most power plants are located pretty far away from residential and commercial areas.
2. The power plant you're linking hasn't been completed yet. Plus, this is a cutting edge design. Most existing plants won't (couldn't?) be converted to this newer efficiency. And for cost reasons, existing inefficient plants aren't going to be shut down and replaced.
3. The fuel cell doesn't require natural gas. It can also run on biomass, which is completely renewable. And since this isn't based on combustion, you don't get the carbon monoxide, sulfurs oxides, nitrogen oxides, and heavier smog causing hydrocarbons. All of the nasties are produced with combustion. Also, since the CO2 is clean, it can be separated easily from the H2O and stored.
4. Well, they aren't burning anything, so 0% has been from burning fossil fuels. I'd guess most of it was from using natural gas as a fuel, but none of it was burned.
One interesting thing I've read is that they are claiming that this is a reversible process, which means it could be used to store PV energy collected during the day and reuse it at night. But, this system produces so much more energy than a PV cell that I'm not sure it would be of much use. You'd need a very large (sq footage) PV installation to generate this much energy.