Soften. Other things that typically are added with salt will tend to toughen the beans, but it isn't the fault of the salt. For decades, chefs have circulated the oral tradition that adding salt hardens beans, but it's a myth.
Several scientific studies verify that adding salt to the soaking water for dried beans will reduce the cooking times. The first and most cited article, originally published in 1977, can be found here. As mentioned in the first answer you cited, the fine folks at Cooks Illustrated found in 2008 that 3 TBSP per gallon of water produces soft skins while not over-salting the interior of the beans. Since you can't see the full article, here is the science according to CI:
"Why does soaking dried beans in salted water make them cook up with softer skins? It has to do with how the sodium ions in salt interact with the cells of the bean skins. As the beans soak, the sodium ions replace some of the calcium and magnesium ions in the skins. Because sodium ions are weaker than mineral ions, they allow more water to penetrate into the skins, leading to a softer texture. During soaking, the sodium ions will only filter partway into the beans, so their greatest effect is on the cells in the outermost part of the beans."
Harold McGee's NY Times blog (August 9, 2008) also notes that adding salt early enough will allow complete penetration of the bean, which improves flavor.
On the other hand, things typically added with salt -- particularly sugar and calcium-rich products -- tend to toughen beans (and the salt gets the blame). This toughening effect is most notable in baked-bean recipes using things like ketchup, molasses, and BBQ sauce. You can bake these beans for days, yet the beans will stay whole and firm. The actual mechanism for this effect is not clear; one hypothesis currently circulating seems to be that these products stabilize the cell-cell "glue" (e.g., Shirley Corriher says so on Good Eats "Pantry Raid III - Cool Beans", transcript online here), but I could not find any peer-reviewed study specifically verifying that hypothesis.
Why infuse the flavor just during soaking? Unless you are eating them just soaked, after soaking you can cook(fry) the pulses with herbs and spices and that will give them a nice flavor. Most Indian Dal curries are made this way.
Best Answer
The actual action of soaking is what does most of the work.
Most legumes have complex oligosaccharides, a type of complex sugar. Digestion of this complex sugar is what causes flatulence. By soaking your beans will help remove some of this excess sugar. Be sure you discard the soaking water.
Though it is often said that adding baking soda helps I've yet to see any verifiable evidence that it would help. Also, don't forget that baking soda isn't tasteless, it could easily add a salty or soapy flavor to your once pristine beans.