Thanks to the info above, I was able to make a tool to unpack the message.bin.
I won't be working on it anymore, so I'll leave messagetool.py here: https://gist.github.com/mid-kid/8279635ee8dc57560e96
It unpacks the message.bin to readable, plain text files.
It mostly works, but there's some rough edges here and there.
I hope somebody can do something with it.
Usage:
Unpacking:
python3 messagetool.py extract message.bin messages_extracted
Packing:
python3 messagetool.py pack messages_extracted new_message.bin