I suppose you could render a custom alpha channel (used as a luminance matte in your compositing/nle app.
Try this:
1. precompose your final comp.
2. apply => effect => generate => fill. fill new precomp with white.
3. create a black solid (comp size). place this layer underneath the first.
4. render this file for use in your nle.
5. apply this new file as a luma matte/key to your jpeg sequence.
This is of course assuming that you want this area of transparency. Considering this is probably going to be a lengthy render you should probably wait to try this until someone else verifies that this is your best option. There are probably plenty other options out there. Hope this helps.
ian