Can the percentage for "1st Period" and "2nd Period" for an open-ended or partial absence exceed the percentage set for "1st Period" or "2nd Period" in the employee's work schedule?

Yes. For example, if the "2nd Period" % in the work schedule is 50%, but the absence request is 75% "2nd Period", then 50% will be taken off the "2nd Period" working hours and the remaining 25% will be taken off the "1st Period" working hours (i.e. the morning work hours will be reduced).