The native version does quite a few extra things, including bringing all the solving tools inside the app (as opposed to using external tools like CyberChef, Boxentriq, Dcode, etc), but also has more compute-intensive operations like creating spectrograms of audio and image manipulation, a much bigger implementation of the Linux terminal, and (safely!) destructive things too – you get local copies of files or databases to work with, so you can delete them, modify them, etc, freely, rather than being restricted to working with shared resources.