There are a number of things to consider regarding these numbers.
From a coffee perspective, it's important to note the difference between caffeine in the bean and caffeine in the coffee drink brewed from those beans. When you extract liquid coffee from grounds you extract some, but not all elements. Caffeine extraction, for example differs based on the brew method.
As the USDA links in the question show, 100g of espresso contains 212mg of caffeine while 100g of brewed coffee contains only 40mg of caffeine. That is because espresso is brewed under pressure, which allows more elements to be extracted from the coffee bean using less water.
On the other hand, to make 100g of espresso you would use much more coffee grounds than you would when brewing 100g of brewed coffee. You might be brewing espresso with a brew ratio of 1:2 (15g of grounds to get 30g of liquid espresso) while 1:16 is a good ratio for filter coffee. In that sense, espresso is just more concentrated, with respect to caffeine but it goes for other solubles (particles in the coffee bean which you extract into the coffee liquid) too.
It should also be said that coffee isn't an exact science. Caffeine content can vary slightly per bean (that's why coffee.org lists the average figures). And another variable that may affect caffeine extraction is the brewing process. Just like different brew parameters (temperature, grind size, pressure, etc.) can affect espresso flavor, they might also affect caffeine extraction. I'm not claiming that any of these brew parameters affect caffeine extraction specifically, but they might.
From a language perspective, there might be some confusion about the description on coffee.org. They describe caffeine content in the average arabica bean as well as the content per 100g of beans. One bean weighs less than one gram, so it might cause confusion. They provide the following figures:
- 1.9mg of caffeine per bean
- 1.2-1.5g of caffeine per 100g of beans
Taking the average of 1.35g of caffeine per 100g of beans, we find there are about 1.35*1000/1.9 = 710 beans in 100 gram of beans.