Observe that “Preferences” is opening instead of the assigned shortcut.
Expected behaviour: Preferences should not be hardcoded to “Cmd + ,”.
Current workaround is assigning whatever you which to execute to something else, and use a macro program like Keyboard Maestro to translate “Cmd + ,” into that command.
Seems like you’re right in this case. Or at least that’s what it looks like. There are a lot of applications that has this shortcut for Preferences, but it’s not possible to turn it off in the Keyboard settings. I’m not sure if it can be overriden on application level or not. I’ll do some investigation.