I'm scratching my head trying to figure out why you're being downvoted while the least well-informed comments along the lines of "Customs officials are dumb!" are at the top.
This is very likely a design patent case, not just trademark. In which case, they could be infringing regardless of the logo on the box.
Then again, the article isn't helping, as it also seems oblivious to the design patent possibility.
I think pinning this to the article is a bit rough, as the press release indicates they think the item is counterfeit, which implies that they're attempting to fraudulently pass themselves off as AirPods. To me, the use of the word "counterfeit" implies a trademark violation. That's clearly not happening, as the box indicates.
If the press release indicated - anywhere - even a whiff of there being a design patent issue (which is subtler and more nuanced than the word "counterfeit" allows for), I'd say it was fair to criticise the article. That's not the case though, and reading the press release, I don't think CBP thought there was a design patent issue either.
Shipping counterfeit products through customs with a misleading box that is then removed prior to sale is a common ploy. And one that CBP is aware of. The box means absolutely nothing here.
This is very likely a design patent case, not just trademark. In which case, they could be infringing regardless of the logo on the box.
Then again, the article isn't helping, as it also seems oblivious to the design patent possibility.