MkvToolNix is certainly a valid solution but the use of other tools increases the mux times.
I have not tried the lines that I have suggested in the previous posts and it is probable that FFmpeg does not read chapter data correctly (using the bluray protocol).
I already have an idea in mind to solve the problem: over the weekend I will try to write a "chapter extractor" which, in a few moments, creates a file that FFmpeg is able to understand.