Just one note to the Mute event. This would works as simple as you mentioned, if you would Mute the only one event in the Track. But, if you have multiple events in the Track, then it’s not so easy. In this case the frozen Wav file is one Wav file for the whole track. Moreover it’s not the whole track. If you have enough space in-between the MIDI Parts, the silence is not rendered. Then in the Wav file, there are specific markers, which says, where should Cubase start to playback this file again. In this case, to Mute one of multiple events is already some kind of process (or you could emulate an automation event, but then you have think of all following consequences).
As I said, it’s doable, but from my point of view, it would also bring some cons.
Maybe you can Render In Place instead of Freeze. Would this fit to your workflow better?