Sharing ARM SWD pins with normal pin function (on Atmel SAM D09 D10 D11)
That will depend on the programmer you are using.
I am actually working with the SAMD20 using the AVRISP mkll programmer from Atmel and you dont have to care about sharing those pins.
The main function of the pin will keep working even if you have the programmer connected there. In fact, that is what ISP means (In system programming)
If you are using the Xplain Pro Evaluation Kit, you can program the device using the USB wire and all programming pins will keep working in their main function.