Hello Mark,
I checked the code of SetPeriodTicks( ). It is changing the Load register of PIT module.
PIT_LDVAL_REG(PeripheralBase,(ChannelIdx)) = \
(uint32_t)(Value) \
This indicates that it should use input frequency and multiply it with the value passed to it.
It should not use the period. I am not sure why you observed it. You might have used something different. But since the code generation through this module will be same, thus it should always use the input frequency.
-Arpita