Can you advise on why you would jumper to the native ESP32 USB vs. default through the CP210x to ESP32 TX0, RX0?
I don’t know the exact reasoning behind making serial USB the default. I’m just guessing but I imagine it’s for compatibility with our other ESP products so that code and tutorials will work across multiple boards but you can always change the jumper if you wanted to use native USB.
If any SFE engineers are in the forum and you know the reason, please comment. 
What I’m really after is what exactly will change if the jumper is changed to be ESP32 native. e.g. Device will not be recognized as a serial device somehow?
Switching the jumper will bypass the CP210x USB to serial chip on the board and connect the ESP32-S2 directly to the USB bus. The board won’t show up as a CP210x serial port anymore and you will probably need drivers from Espressif to get the ESP32-S2 to show up as a device on your computer. (It will most likely show up as another serial port but might show up as multiple other devices.)
We don’t recommend you change this unless you know exactly what you’re doing and you’re using Espressif’s IDE, we can’t currently support the board when it’s not in CP210x mode.