Pcapng is an evolution from the pcap format, created to address some of its deficiencies. Namely, the lack of extensibility and inability to store additional information. Any file that uses comments, multiple interfaces, or saves name resolutions MUST be a pcapng file. These are some of the features that the pcapng format enables.
For deconstructing pcapng structure, I would consult Sam’s Browne’s wonderful article on the subject.