Hi Steve,
In our last conversation it was concerned with flats (I thought). Now you have a different resample question.
ImageRegistration through StarAlignment does not require the images to be the same size. I typically produce combined R,G,B images that I register with a larger luminance (reference) without resampling.
1. So I think the answer to this is no. You can combine your 2x2 images...and then you will have 4 images. 3 images (RGB) that are 2x2 and one (luminance) that is 1x1. Just align these 4 images with Dynamic StarAlignment with the luminance as the reference.
2. Based on my suggestion above- why not align with your combined luminance (that is calibrated, cosmetically corrected, and has the best S/N)? I think this is the way to go.
-adam