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Most of these flights are on so small airlines that it's hard to get historical performance data on but the Philippine 453 flight out of 34 observations, 85% was on time, averaging only 9 minutes of delay, maximum 31 minutes of delay. So yes, the schedule is pretty firm.
Rome2rio does show some bus connections but it's 1.5-2 days and does not show a significant savings over a flight taking less than 2 hours so I have not pursued this avenue further.
On further research I have found some outdated information on ferries going from Manila to Iloilo and on to General Santos taking even longer closer to three days. I haven't researched this either but the Wikipedia page on 2GO reports it to be a modern fleet so one can presume it's on schedule.