So, I'm totally not a lawyer, but I find the vagaries and nuances of law fascinating. Perhaps I can help clarify some details.
First, he was at an airport and had not yet been permitted entry to the USA - in a sense, they were still in "international waters." The government maintains that anyone entering the country at a border may be subject to warrantless search by 19 USC 482 which was originally to allow searching of boats to seize any contraband. CBP doesn't need to have probable cause for the search. Further, the government maintains this search is exempt from 4th amendment protections by historical judicial precedent (or something) called the "border search exemption." This has been challenged in some districts but has not yet been considered by the supreme court.
Second, he's not charged with 18 USC 1519 "Obstruction of Investigations by Destruction of Evidence" but rather with 18 USC 2232(a) "Destruction of Property to Prevent Seizure." As I understand the distinction it's that as the CBP search isn't a part of an investigation based on a probable cause to believe a crime has been committed, they aren't searching for evidence of a crime and thus there isn't evidence to destroy. 1519 is far more serious and can mean up to 20 years in prison vs 2232(a)'s 5 years in prison.
The statute is broad enough to apply if the act was done at all but it does need a search to happen. Specifically, "before, during, or after any search for or seizure of property." From what I'm reading, you're welcome to wipe your phone if they don't search it.
As to corporations routinely destroying evidence, that doesn't mean they're not committing a crime, but I do believe there has to be intent to obstruct an investigation regardless if an investigation exists to obstruct.
The "border search exemption" mentioned far above is why no search warrant is needed for him to be charged with this crime.
If he wanted to prevent the phone being searched and not be charged with 2232(a), then he should have surrendered the phone to them and refused to provide an unlock code. Yes, that means they likely would have kept the phone and, potentially, indefinitely. A US citizen may not be denied entry to the USA.
Had he not been a US citizen, then refusing the search OR surrendering the phone and refusing to give the unlock code _may_ likely have been grounds to refuse him entry, but that's still not charged with a crime.