If I checkout/download dataset D on a new machine, it will have to download/extract 15GB worth of data instead of 3GB, right? At least I cannot imagine how you would extract the 3GB of individual files out of zip archives on S3.

Yes, I'm not sure there is an interface to extract only partial files from the zip (although worth checking).
I also remember there is a GitHub issue with uploading 50GB dataset, and the bottom line is, we should support setting chuck size, so that we can upload/download smaller chunks of the entire dataset. wdyt ?