These news are about the military inquiry. That is why it doesn't metion the pilots charges. And those news doesn't mention:
"For the pilots, the following procedural failures can be listed, besides that indicated as determining:
• the lack of proficiency in the handling of the Embraer Legacy aircraft, especially in the operation of its avionics, characterizing incompetence;
not using the communications failure code on the transponder;
• not using the emergency frequency in due time when the communications failure
was characterized;
• conducting the aircraft in an imprudent manner and being negligent of security rules; and
• the low situational awareness of the Legacy’s crew."
About the clearance:
"An ATC clearance means an authorization by ATC, for the purpose of preventing collision between known aircraft, for an aircraft to proceed under specified conditions within controlled airspace. It is not autorization for a pilot to deviate from any rule, regulation, or minimum altitude nor to conduct unsafe operation unsage operation of the aircraft. The pilot-in-command of an aircraft is directly responsible for, and is the final authority as to, the operation of that aircraft. If ATC issues a clearance that would cause a pilot to deviate from a rule or regulation, or in the pilot's opinion, would place the aircraft in jeopardy. It is the pilots responsibility to request an amended clearance."