It seems FFMpeg is used for audio conversion such as flac pcm or wav output. Looks like this release of MakeMKV doesn't get into video compression. Also 1.7.8 includes 32 and 64 bit versions of FFMpeg. Sorry I gave the wrong info. I just surmised by looking at the settings dialog(always dangerous.)
For video compression it looks like BDRB or some other is still required.
It does have profiles for controlling things such as audio output, stuff to do with subtitles like forced,default etc.. setting an audio track as default yadda yadda.
There's a subforum on the MakeMKV forum for advanced usage. What profile settings are available and how to use etc..