So far as space is concerned, the rootfs is the size of the entire Jetson root file system install. It is actually more than this, as you start with the tar.bz2 and unpack it, so you have both the compressed archive and unpacked version; then there is the creation of a loopback mounted full file system, which copies this yet again, based on boot files and sample rootfs; finally, a sparse system (essentially compressed variant of loopback) is also created. File system use on host definitely exceeds rootfs size substantially.
Once sample rootfs is populated, the tar.bz2 archive could be deleted. Once the sparse file system has been created through the first flash, it should be possible to delete the uncompressed loopback image and tell it to re-use this sparse image for future flashes (assuming no parameters change). So long as you re-use the image you could even delete the content of the sample rootfs directory. For reference, system.img.raw is full-size uncompressed loopback mounted file, system.img is the sparse/compressed image which could be re-used.
I do not have an Ubuntu system so I do not use JetPack and do not know what issues there are for mixing CUDA 6.5/7.