Just an idea - why don't use standalone MKVToolNix binaries (mkvextract, mkvinfo, mkvmerge) instead of full MKVToolNix GUI app? This may save about 70MB of space.
I done few quick experiments and deleted everything but mkvextract, mkvinfo, mkvmerge from MKVToolNix.app and seems it can work in Hybrid like this.
Seems it also works if i delete MKVToolNix.app and simply put mkvextract, mkvinfo, mkvmerge directly to MacOS folder. Seems Hybrid can "see" those components there automatically:
Can you deny or approve this idea?
P.S. There is also explanation in MKVToolNix readme.txt file:
"If you need the command line tools then copy mkvextract, mkvinfo,
mkvmerge and mkvproedit from ./MKVToolNix-51.0.0/Contents/MacOS/
to /usr/local/bin"