Does the SAMD21 have pullups on every pin?

Yes, the ATSAMD21 family of microcontrollers has internal pull-ups (and pull-downs) on every Port A / Port B pin (like PB03 or PA14) except PA24 and PA25. You can enable or disable the pullups in software.

The RESET pin also has an internal pull-up which is always active and can’t be disabled.