Yes, this is how it's implemented at the moment. I went that route to be most compatible with foobar2000, which is using a similar approach (at least at the time). It's basically a representation of the chapters in Nero form — your original chapters are still there.
No, it's currently not possible.
This was a different issue that has been fixed with v2.93a. Back then, Mp3tag created the chpl atom in that case no matter if chapters were present or not.
[2019-01-29] CHG: chpl atom was created if Apple gapless data was present. (#44323)
It's an addition of the Nero representation. No change of the existing format.