Coercion was the reason from start, it's explained in the article.
"A motion filed by his defense argues the interrogation focused on child sexual abuse material as a pretext for investigating his connections to the protest movement."
So the message was simple: don't protest and you will be not harassed.
A blank phone is suspicious in and of itself and probably invites more questioning and suspicion.
And from personal experience, once a border guard is suspicious of you and you're a non-citizen, you're fighting a losing battle to get into that country, regardless of whether you're doing anything shady / illegal.
The most straightforward answer I think is to use common apps for more commonplace social media activities and separate apps that can be removed from your phone when you're crossing a border for things you want to keep private. It's not perfect privacy, but I think a border is one thing that for better or worse you'll need to accept some compromises on.
"A motion filed by his defense argues the interrogation focused on child sexual abuse material as a pretext for investigating his connections to the protest movement."
So the message was simple: don't protest and you will be not harassed.