[Cin]Compositing two layers with transparency and chroma key

I want to achieve the following animation: - Track 1: the CGI animation, it has transparency and a chroma layer - Track 2: Video the animation runs over - Track 3: the CGI animation transitions to Track 1 + 2 = the default operation, this works when stacking the animation on top of the video. But *without rendering twice*, how am I able to mask out the chroma key in the animation, so track 3 becomes visible under it? -- Stefan