Proposed workflow:

1. aligning images
   1.1. choosing reference frame (may be one, may be tree-like as well)
   1.2. aligning to reference frame
   1.3. saving aligned images to temp space
   1.4. optional: saving transform matrix to a file as aligned image description
2. averaging aligned images
   2.1. averaging images in such a way that regions which do not overlap in all images are not more transparent or darker
   2.2. saving averaged image with high bit depth
3. optional: color corrections, sharpening