That makes sense if you are not using the other features I guess but don't you run into the same issue with your custom features or do deploy them separately? If you deploy separately it seems that since the features depend on the core they will have the core dlls in their own bin folders and this will be redeploying those files with each feature unless you clean them out to make packages of just your features. This is what I do when I package my add on products.
I will do my best to try and keep all the files in the core project "included", just let me know if I miss any and I'll update them quickly.
Best,
Joe