You can use MKVToolNix's very own CLI exe's to batch remove the Header tags (like the Header's Title counterpart) fast and easily without remuxing.
For example, if I have a few MKV's inside a particular folder, I use something like below. This should remove the header title, by simply putting no value after the equal sign.
for %Z in ("*.mkv") do mkvpropedit.exe "%Z" --edit info --set title=
I highly recommend using MKVToolNix's CLI exe's instead of FFmpeg's because in my experience, FFmpeg removes or rearranges existing tags, or adds some unnecessary tags like stats and duration. I use FFmpeg to remux media files in the beginning, like after I have downloaded YouTube videos. Then I use MKVToolNix for final remuxing.
For example, I have finished tagging an MKV file with Mp3tag and the other apps, but after I remuxed it with FFmpeg, the tags displayed in MediaInfo is different from what I originally intended. Even by extracting the tags to an external XML file, it is different.
Also if I may add, for anybody. I recommend remuxing those downloaded MP4's and WebM's from YouTube using FFmpeg first to the same format, then tag those instead by Mp3tag and other taggers.