Replying to my own post here…
Looks like there really would be no way to do this, as Boris FX would need access to both tracks. More of a compositing thing than a track fx thing.
I guess I can either stick to static plates and just reference them directly in the Boris sub-project, or pre-cut both exactly right and bring the motion plate into the Boris sub-project.
Thanks for reading though =)
CraigL