Okay, according to MediaInfo, the original was muxed using mkvmerge 71.1 and the new version used 81.0.
The video steam, the audio and the subtitles steams have the same size in both.
Like I suspected, this is probably caused due to some additional indexes mkvmerge added in newer versions.
I suspected this was caused by one of the options under: 'Config->Containers->MKV' but that was not the case.
Also, simply remuxing the file with mkvmerge resulted in the same file size as the original.
After some searching, I found what is causing the majority of the difference.
Hybrid uses '--compression -1:none' for compatibility,
Quote:--compression TID:n
Selects the compression method to be used for the track. Note that the player also has to support this method. Valid values are 'none', 'zlib' and 'mpeg4_p2'/'mpeg4p2'.
The compression method 'mpeg4_p2'/'mpeg4p2' is a special compression method called 'header removal' that is only available for MPEG4 part 2 video tracks.
The default for some subtitle types is 'zlib' compression. This compression method is also the one that most if not all playback applications support. Support for other compression methods other than 'none' is not assured.
see:
https://mkvtoolnix.download/doc/mkvmerge.html#2.8'
using 'zlib' instead of 'none' caused the size to shrink to 94.7MB (original: 92.3 MB), so there are still 1.6 MB difference which are likely caused by one of the options under 'Config->Containers->MKV'.
I thought that 'Config->Containers->MKV->Disable header compression' would disable the addition of '--compression -1:none' but there are some additional internal cases in which the headers get still added. (not sure why these are there)
=> will look into it more tomorrow.
Cu Selur