Running it through any encoder such as Handbrake will recoding resulting in quality loss. Not to mention time consuming.
This is fine if you want a smaller file, but to simply change from MKV to MP4 you only need to demux/remux the audio video streams which takes just seconds.
I ahve a different way which works well:
You will need two free applications for this.
1) MP4 Box MP4Box 0.5.0 - VideoHelp.com Downloads
2) YAMB (You do NOT need the Installer version) Yamb » Yet Another MP4Box UI
Both are free. You need YAMB if you do not want to use mp4box as a cmdline. Plus YAMB just makes the whole thing simpler.
Down load both.
-Unzip YAMB to a location you want it.
Open YAMB, and go to Settings/ Advanced
Point it to the location of the MP4box exe and choose a location for temp.
Now you just Open YAMB, select create MP4 and add your MKV file. And in less than a minute your have the file in a MP4 container with 0 quality loss.
As far as the terminology, if I understand it all correcly:
ENCODE/RECODE - Taking a file and completely recoding it to a new format, or the same to reduce file size or change codec formats.
TRANSCODE - Decoding and streaming in alternate format
DEMUX extracting the audio & video streams from a container into thier raw formats. Such as (MPEG,H264 AC3,DTS,AAC etc)
REMUX or MUXING taking the raw video/audio streams and putting them into a container (such as MP4, MKV, AVI) to create a useable video file.