Hi,
During and after reset almost all GPIO pins are in high-z state, until you configure the PCR registers, for example weak pull-down/up etc.
The PWM module control the output once the PA field in PCR register is set for PWM function and when PWM.OUTEN register is configured. In that case the polarity of the PWM output is done by PWM.SUBx.OCTRL[POLx] bits.
Regards,
Petr