1. MakeMKV this is post does not support filters.
2. MakeMKV only takes the selected streams and saves them to into a MKV file(s).
3. Handbrake, Xvid4PSP, Super, etc. Are all 3rd party programs that will/can act on a MKV produced by MakeMKV.
Here is a simple run down (example) of how to compress a the streams in a MKV.
1. Use MakeMKV to convert your disc into a MKV
2. Open any 3rd party converter software what supports all reading (INPUT) a MKV with the stream types inside AND has the ability to OUTPUT to a file type you want (most likey a MKV) with the streams converted to what you want.
INPUT : mkv, 2 steams (1 mpeg2 (Video), 1 ac3 (audio)
OUTPUT : mkv 2 streams (1 h264 (video), 1 aac (audio)
3. Setup said 3rd party software to OUTPUT/Convert/Save said file to what you want (aka to taste)
4. start the conversion
5. Check said OUTPUT file to make sure you like the quality and there are no audio sync issues.
6. Remove said INPUT file, if you want.
OR to put it more simply:
1. Covert Disc to MKV(s) with MakeMKV
2. Convert created MKV(s) with 3rd party software.
But in no way can you have MakeMKV compress/convert the MKV for you during OR after it's creating the MKV(s).