How to calculate the overhead of wrapping multiple elementary streams?
The only exact approach is to simulate the muxing. On a *nix system this would be

ffmpeg -i i.mkv -i i.flac -c copy -map 0:0 -map 1:0 -f matroska /dev/null


At the bottom of console readout, there's this line:

frame=152217 fps=71723 q=-1.0 Lsize=  551301kB time=01:41:28.66 ...


The Lsize is what you want. This operation is pretty quick as there's nothing written to disk.