How it overwrites my sidecar [Name] values is complicated, but long story short, it happens when I move files and they are re-imported.
The obvious solution would be to use the MC "Rename, Move, and Copy Files" function to move the files. Then they won't be reimported, and so the [Name] tag won't be overwritten by the MKV Title metadata. But I guess your long story may explain why that isn't possible. I think you may have explained that previously. Recording on one server, transferring to another, and importing there?
MC is doing the correct thing when reimporting, BTW. In all metadata research I have done the Title field is the source of the [Name] tag for MC. Most metadata doesn't have a "Name" field. It is almost always called "Title", or some variation of "Title", as you noted.
A quick solution for TV Series would be to select all the affected files and run the "Get Movie and TV Info" function on them, as long as the [Series], [Season], and [Episode] tags are correct, which means that data would need to be in the file name for CARNAC to extract during import, or in the sidecar file you copy across with the MKV file.
I did read in the forum somewhere what gets priority for tag values, the tags in the files or the sidecar file. But I can't remember now which it was. Perhaps a search would find it. If the sidecar has priority, you could change the setting in "Options > General > Importing & Tagging > Sidecar tagging mode" to save tags in both the file and the sidecar file, and then MC would respect the [Name] tag in the sidecar file over the metadata in the file. Worth some research or testing.
But it might be good if MC supported writing tags to MKV files where that is possible, instead of or as well as putting them in the sidecar file. If there was a good standard for writing metadata to MKV files. The [Name] tag is supposed to be written to the file, if possible, and it doesn't seem to be as none of my MKV files seem to have the Title metadata in them. So it is a bit strange that it reads the metadata field on import. Sort of half a solution.