I think Rob is working with mono channel data, then the Halpha debayer mode is useless @supernov.
Yes, process the channels seperately Rob. Registration can be simply done when you have the stacks ready. Just load the stacks and register them and save registered frames.
Or another way.
Calirbate all you lights first and save your calirbated lights. Then load all lights of all channels and register them. And save registered frames.
Then you can stack all channels separately using registration mode: no registration
There are several ways to do this.
In the future, we can try to make a batch mode tool for this, I believe Yves mentioned this to me already ;-)