cpu/samd21: Avoid clearing interrupt bits unintentionally

The INTENSET, INTENCLR, INTFLAG registers are write-1-to-confirm
registers, so writing zeroes will not affect anything, on the other
hand, a compiler generated read-modify-write cycle may unintentionally
affect more bits than the one being set. Avoid by using direct
assignment instead of or-assignment (|=) or bitfield writes (.bit.xxx=).