I've had the pleasure of talking with Renaud from Tenable about the Nessus Transport Protocol lately. I was getting frustrated because I only had the 2.x code to reference, and wasn't sure if 3.x was significantly different. He was very welcoming to my plight though and answered my questions as best as he could. It reassured me that Tenable is not evil.
I'll post some of the things I've observed about NTP so that others may be less confused.