Is there a way to render a 3d stereo movie within Sequencer?
Yes. Render one eye with a SceneCapture2D and comp it in a post process. 
I’m working on a tutorial that I will post here: https://www.facebook.com/groups/1045465492195829/
SceneCapture2D can do it, but has some limitations.
I tried the old “-emulatestereo” with Sequencer, it did not work.
nVidia Ansel plugin has a very good solution for this and can capture normal stereo and 360 stereo with gourgeous quality. But it seams that you can not control it to shot frame by frame within a blueprint.
If it is possible, it would be the perfect solution.