Thanks for reporting the issue with the newly added Nero chapters are using the global tags title instead of the chapter titles of existing QT chapters.
I've created an internal unofficial build of Mp3tag for you which should fix the issue:
Regarding Mp3tag not being able to write or update existing QT chapters — Yes, this is a limitation of the feature. As I've mentioned in the changelog:
[2019-01-06] NEW: added support for reading and removing QuickTime chapter information.
Writing QT chapters is on my internal wish list.