I've searched extensively for a solution to this and still nothing exists. I've even asked the creator of Matroska Tools, but his response is that he doesn't like programming GUIs. His Command line solution mkvpropedit is extensive, quick, and is easy enough to use, but is for single files only.
For people averse to the command line and don't use VLC, you can use the mkvmerge GUI "mmg".
File > Header Editor (CTL+E)
Drag-n-Drop a file into the new window
Segment Information > Title
Title is the only real tag I'm interested in which allows for clean playlist entries instead of the filename, but you can edit titles for all the individual tracks as well are changing the default order of multiple tracks, and more. All without remuxing. When you are satisfied with the changes, CTL+S to save and drag the next file to the window for editing.
It's a shame that no one has picked up the torch yet for tagging MKVs, and I feel that it is really holding the format back. There is a great demand for a solution and whoever solves it will probably have a huge influx of users. I'm just hoping it isn't crappy commercial company that doesn't care or listen to the community of users.
As a Linux user it might seem strange posting here, but as this program is peerless for media tagging, it is still just one of the 2 windows programs I can't go without. I am genuinely hoping you might reconsider looking into adding mvk support in the future.