You must start the external oscillator via software. I used this on my Arduino Zero clone
/*****************************************************
start external crystal XOSC32K, must disable first
*****************************************************/
REG_SYSCTRL_XOSC32K = SYSCTRL_XOSC32K_STARTUP(0x7) | SYSCTRL_XOSC32K_RUNSTDBY | SYSCTRL_XOSC32K_AAMPEN | SYSCTRL_XOSC32K_EN32K | SYSCTRL_XOSC32K_XTALEN;
REG_SYSCTRL_XOSC32K |= SYSCTRL_XOSC32K_ENABLE;
while((REG_SYSCTRL_PCLKSR & (SYSCTRL_PCLKSR_XOSC32KRDY)) == 0);
The clocking mechanism on the SAMD21 (and pretty much all ARM Cortex MCUs) are a tad more complicated than your AVR chips