Mp3tag will create Nero chapters if it encounters QT chapters. It's because, while it can read QT chapters, it can't modify them — it's not a complete remuxer like ffmpeg is.
Previous versions of Mp3tag however (up until Mp3tag v3.31b I've just released), also copied artist, album, and other metadata to the Nero tags and prioritised those when reading.
This is now different, because it tries to create a minimal version of the metadata for the Nero tags (mostly title and track number). Every other "global" data is kept in QT tags and will be read and updated by Mp3tag and external tools.