That's true but outside of the sports arena people have always worn some sort of foot protection.
Footwear is one of the greatest components of both ancient and modern military. Even poor people who couldn't afford shoes would be able to craft at a minimum a sandal.
I think a lot of theories will fall short if you only look at martial arts from a sports perspective. Especially when it comes to "Why things are done a certain way." Kicking with the ball of the foot is simply a safer kick and it can withstand more force and weight than the other option of kicking with toes.
Think of it this way. When you jump you land on the ball of your foot. That same bend in the toes as you land is often the same bend in the toes when people kick with the ball of their feet. You can land on your toes if you like but I don't recommend it.
I personally think training with shoes on is more realistic than training with shoes off. All the street fights I've had I had shoes on. All the conflicts and heated arguments I've been in were with shoes on. Some people wear shoes almost as long as they wear underwear. Some people wear shoes to work and then come home and slip on a different pair of shoes. At the time of this message I've been wearing boots since 6:30 am. it's now 7:45 pm.