We'll start with the worst one (right rear):
Yes, that rectangle is some bare metal. The only explanation I can think of is that when the car was painted at the factory, this was one of the points where they supported the car body as it went through the paint line. The color of the car is Dark Slate, and it was built at the Canton plant. On most of the car, the primer is mostly a tan/olive color, although in these areas the pure primer looks more of a light gray. On most of the underbody, you can see the overspray from the Dark Slate, but in the area around the bare rectangle, there's no overspray. So they never went back and primed/painted the original support points.
Next up is the left rear corner. This rectangle had some partial coverage, but there's still plenty of bare area.
Next up are the two front corners. They're not perfect (they have some conductivity), but they just look scuffed up rather than actually having skipped a step at the factory.
The large oval holes (front and rear) and front squarish holes had also been scuffed/scraped through, in various places along their inside edges. The purpose of the oval holes is for things like winch hooks when the the car's being pulled onto a flatbed, so they may have already been used for that kind of thing, either at the factory or when the car was transported.
As mentioned above, at any place that looked like it might be bare metal, I checked resistance with an ohmmeter to see if it really was. This was with the other probe on a bolt head (on a bolt that actually conducts to the car body; not all of them do, so check the bolt against another bolt first). The somewhat disturbing thing was that, in addition to these obviously bare spots, there are edges all over the underbody that also show some conductance, such as the various round holes that the car has all over the place.
Here's an example of checking an edge - I'm not pressing hard or using the sharp tip of the probe, just sliding it along an edge and watching the meter, or listening for beeps.
Now I already know that paint generally doesn't form a good film along sharp edges. It might have been nice if they took the time to round all the edges a bit at the factory, before painting the cars, although I'm sure this would raise the price of the car a fair amount. To see if conductivity along edges is normal for other cars, I also did a similar test of my 1992 Plymouth Laser (from California so it has no rust), since those cars seem to hold up at least as well as average in northern climates with salted roads. The Laser also shows some conductivity along edges, although maybe to a lesser extent than the Altima. So I guess this is somewhat normal.
After most of these pictures were taken, I mixed up a few small batches of epoxy primer and did some touchups (you can see the gold topcoat that I used in the last picture). It might be a good idea for other Altima owners to check this out to see how your car fared in these areas.