Wade,
I think what Jack means is that, say you have 10 images (image01, image02, . . ., image10). You establish that, say, image07, is the 'best' image of the bunch. You COPY that image, and rename it as RegistrationMaster (or whatever). This STILL leaves you with the first 10 images - which you then align against the RegMaster. Obviously, image07, being identical, will not 'suffer' during the registration process - but it WILL be included.
So, you still end up with ten 'aligned' images, ready for further processing - such as ImageIntegration.
You also now have a specifically named 'master' image that you can add to the other 'master' images that you generate as part of your pre-calibration steps (MasterBias, MasterDark, etc.)
Is that any clearer?
The only downside - if it is one - is that you sacrifice a tiny bit of HDD space to hold an 'identical copy' of only ONE of your other images. But it does have the advantage that it then becomes absolutely clear what the 'position reference' for the final image is - and it can even help get your scope alignment 'just right' if you have to split imaging over multiple sessions.
Cheers,