Rendering a custom render pass will render the viewport.

If close the "Sequencer" window while leaving the "Render Movie Settings" window open, and then click the "Capture Movie" button, you will capture the movie from the perspective of the CameraCuts track registered in the sequencer, as expected.
If the "Image Output Format" is not "Custom Render Passes", there seems to be no problem.

1. Create a new LevelSequence asset and add the appropriate CameraActor and CameraCuts tracks.

2. Open the "Render Movie Settings" window.

Change "Image Output Format" to "Custom Render Passes" and add "Final Image" to "Include Render Passes".

4. Press the "Capture Movie" button.

5. You will see that the editor viewport has been captured instead of the result specified in the CameraCuts track.