According to the LA times article, barefoot runners naturally strike with their toes, whereas people wearing shoes tend to strike with their heels. If you strike with your toe you have a lot of shock absorption due to the lever arm. It seems like a natural thing to do.
Heel strikes on the other hand transmit the impact straight through the ankle, the knee, and hip joints. Clearly that is not so good. To compensate the shoe takes some of the impact but on the whole the situation is probably a lot worse than striking your toe. It is of course possible that you can adapt to heel strikes. The body does remodel itself constantly and if new stresses appear, adaptation takes place.
Obviously lots of people are heel-strikers and you could argue it works for them. But then again, lots of runners get injured. So much so that injury prevention is a key worry for runners. Runners are much more obsessed with injury than bikers or swimmers. And for good reason. According to one recent article in the NY Times, more than half of all runners get injured at least yearly. That is a lot of people.
I do think my position changed when I ran 11.5 miles with thin soles. I did use my toes and forefoot a lot more. When you have no cushioning, striking your heel is not pleasant. Also when there is little weight on the back of your foot it is easier to "fall" onto your forefoot. It seems almost a no-brainer.
I am sure that is why the soleus is stressed. It simply isn't used to this position and I went from essentially zero (i.e. 0.5 miles) to 11.5 miles in one fell swoop.
Today I rode on rollers for 1:15. I rode pretty hard. Interestingly enough riding does not put any additional stress on my sore calves. I must be using different muscle groups to ride. That much is for sure.