Once arrested he had to be taken before a federal magistrate within 48 hours. A mandatory part of the proceeding is an advisement of his rights. I don’t know why FBI and DOJ are hanging the judge out to dry on this, but I have a feeling it has to do with their bungling of the Russian FSB leads and the so-called “investigation” of his brother.
Arraignments are usually held before magistrate judges, depending on local rules and pradcice.
I may be wrong about this, but I think the FBI's problem is 16 < 48. They, like you, me and everybody else, thought they had 48 hours. DoJ jumped the gun by more than a couple of hours. Maybe they did it out of ignorance or stupidity, but the DoJ still had time to operate without slamming the door in the interrogation.