Mkvtoolnix-gui.exe command-line parameters

When calling mkvtoolnix-gui.exe from the command line with multiple source files, is there a way to override the “Adding files via drag & drop or copy & paste” dialog and specify (on the command line) that I want them all to be added to a single new multiplex setting?

I looked a little at using a .mtxcfg file, but I can find no documentation on its structure, and the only way I can get one to examine is to create one myself, which is extremely verbose and unwieldy (no line breaks on Windows). I’m hoping there’s a simpler way.

No, there isn’t. It uses the same logic as if you’d dragged & dropped a bunch of files onto it, with the same options available in the preferences applying to both methods.