1. The government considers people trying to enter the U.S. to still be outside the U.S. so the government argues that constitutional protections do not apply (i.e. they do not need a search warrant). I would then also ask then how do U.S. laws apply? How can the U.S. government charge a person with destroying evidence when he is not yet in U.S. jurisdiction?

By the time you hit Customs, you're already in U.S. jurisdiction. I mean, generally you're in U.S. jurisdiction once you enter U.S. airspace and land. Whether you have been granted entry to the country can be a bit more nebulous when you arrive at an internal "port of entry." But that's not going to be an issue in this case. In nearly all U.S. international airports, you clear immigration before you hit Customs, and Atlanta is no exception.

2. What would be interesting is using a phone operating system and code that would delete personal data on the phone (like this person here had) but then cross the border with zero personal data on the phone. So when the border guard asks for the pin you give it to them and the phone deletes everything/nothing. How can they charge him with destroying evidence when nothing was destroyed? I guess this is a long roundabout way of asking, doesn't the government have to actually prove something was destroyed?

They do have to prove it, but they can prove it using circumstantial evidence. Namely, that literally no one bothers to carry their own personal cell phone with zero personal data on it - ever. So that the only reasonable inference from the fact that the cell phone had no zero personal data on it after the agents were given the code was that the owner did, in fact, utilize the "wipe" code function that the OS had. The complete lack of data on the phone is proof that the owner gave the agents a "wipe" code to destroy data, because there is no other reasonable explanation.

It's the same type of circumstantial proof they use if they, for example, catch you with a package of cocaine in your pants pocket. You can say that someone might have broken into your apartment without your knowledge and placed that package of cocaine in your pocket and you didn't realize they did it. But the government doesn't have to disprove such an unlikely scenario. The fact that the cocaine is in your pants pocket is sufficient evidence that you were knowingly in possession of the cocaine, because the existence of fanciful possibilities doesn't create a reasonable doubt to counter that evidence.