MKVToolNix has no "CFBundleIdentifier" key in its Info.plist on macOS
according to Apple, the "CFBundleIdentifier" in the Info.plist file is required for each app ( https://developer.apple.com/library/archive/documentation/General/Reference/InfoPlistKeyReference/Articles/CoreFoundationKeys.html#//apple_ref/doc/uid/20001431-102070 ), still MKVToolNix doesn't have any bundle identifier.
i'd recommend adding
<key> CFBundleIdentifier</key> <string>org.mktoolnixteam.mktoolnix</string>
at packaging/macos/build.sh around line 550