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If you chose ES (Elemental Streams) for your output type, you would get a separate video M2v and a audio Mp2 file. I'm not sure what the 'movie clip' is. That sounds like a Windows designation. If you chose 'System (Video+Audio), you would just have a MPEG-2 with a Mp2 audio track muxed in. If you are using TDA to author, it can accept elemental streams, so either way should work.
EDIT: Have you unchecked 'Hide extensions for known file types' in 'Tools>Folder Options>View? Otherwise you are likely not seeing the true extension.