Was looking at the feature wishlist,
this one looked interesting for audibooks:

• Add chapter metadata for .m4a files using ffmpeg-bin.

I've checked the docs, and it seems that libsndfile doesn't support m4a/m4b format,
see libsndfile/libsndfile#389

However, ffmpeg does, as you mentioned, and using a command line ffmpeg
ffmpeg -i input.wav -i chapters.txt -map 0:a -map_chapters 1 output.m4b

and having chapters.txt as

;FFMETADATA1
[CHAPTER]
TIMEBASE=1/10
START=0
END=7164
title=Chapter 1

[CHAPTER]
TIMEBASE=1/10
START=7165
END=25329
title=Chapter 2

inserts the chapters into the file - I see them in VLC in Playback->Chapter->Chapter 1/2.

Generating this file isn't that hard, and adding it to the conversion would work,
there's a ffmpeg-python wrapper (https://github.com/kkroening/ffmpeg-python),
the user would need to have ffmpeg installed.

I'm not 100% sure how to do it in the wrapper, but for a prototype I could directly call ffmpeg.

I'll make a prototype in my fork and then we can check it out.

Cheers