The problem isn't adding yet another checkbox to the Qt UI. It's the amount of things to do for each such configurable thing:
- Add checkbox in preferences dialog (trivial, it's one line in the corresponding .ui file)
- Determine keyboard shortcut that isn't used by any other visible control for English & German
- Save that setting in the configuration
- Add a corresponding command line option to mkvmerge
- Add help output for the new command line option
- Add documentation in mkvmerge's man page
- Implement both the warning as well as having it turned off in mkvmerge
- Implement test cases for all three cases (other MIME type, bad MIME type with warning at defaults, bad MIME type with warning turned off)
- Update the program & man page translations
- Translate all the new content into German
- Add a NEWS entry
Nothing about this is hard. It's just tedious & takes time. Nothing about what you've said would reduce the amount of work I'd have to do.