@Florian Can you elaborate on this?
By "Apple gapless data" are you referencing the legacy ITUNESGAPLESS pgap field that needs to be set to 1? While I don't believe current versions of iTunes specifically uses this any longer, it can still be used and set in mp3tag if that is what is required for keeping the chapters from getting generated.
In the case of the OP's concern, is the indication of "MP4 NERO" just a change of format based on how mp3tag handles chapters in m4a? I don't think there are other specific tags added, just the format change, correct?