MultiAVCHD should be an option in BD Reauthor Mode. There’s even the potential you could swap out the video from the mkv into the Bluray, since it is technically BD-Compatible.

Were the original audio files used or did you render new ones that were Encore Compliant? (this could have an impact on video or audio swapping)

Edit: just saw the video question posted. Many authoring programs are very strict about which files they will accept (DVD Architect is awful about this) - I’d imagine this is to ensure maximum compatibility and avoid extra troubleshooting questions of “I rendered my project, why won’t it work”