If you use top video track it will only export the current top layer of the selected version layer (which is set as primary). So looking at your screenshots, it looks like your bottom version is the primary (selected) version, this is the version that will be exported. Also I see Include Alpha is not enabled, I dont know what your DI pass is exactly but normally I would enable that one.
I never done it this way, but if it’s only 1 matte channel, I would include in in a batch render output ( Set batch render node to multipass and pipe the matte channel in the second input. Then export this new clip the way you did (but with including alpha)