What is mkvtoolnix doing?

[hwh]

Hi, sorry if this is a stupid question, but I am sure people here know.

I have some MKVs created by OBS. For some reason I picked up this software a couple of years ago, maybe to have a look at some issue with an MKV I had. I noticed it generated a much smaller file than the source.

In other words I "multiplexed" an MKV file with nothing to create an identical MKV file that is like 50MB smaller. I don't know why. And since it's meant to be lossless and acceptable for editors and uploading and so on, I don't want to do something weird to the file to make it unusable.

I also experimented with a very similar file which was remuxed to MP4. Running this MP4 through mkvtoolnix again yields a file about 50MB smaller. I can't find anything wrong with these smaller files but I am suspicious and don't really want my files in MKV anyway. I just don't see why the MKV -> MKV process does anything.

If I remux the MKV mkvtoolnix made back to MP4, it only gains 3MB. So, I just want to know what the hell it's doing to my files that isn't video related. Apparently some kind of bloat is being removed. But is it innocuous?