Is it really necessary to manually clear the XMEGA timer overflow interrupt flag?
Is there a scenario/reason where manually clearing the flag may be
  required?


Not sure about the ASF, but there are cases where you need to cancel any pending interrupt. For instance, when (re-)configuring a timer you may want to disable interrupts, modify the timer, and cancel any timer interrupts which may have occurred in the mean time, before re-enabling interrupts.

If you don't even have an overflow ISR you can still poll the OVIF to detect overflow, and reset the flag to arm it for the next overflow.