I would say that it is not common for flights to be cancelled, but it is not uncommon for flights to be delayed for hours (or for you to be put on a later flight). All that being said, since there are only a couple of flights a day from PP to MNL, it is more likely to be cancelled than delayed. Sorry, no crystal ball here. I have seen a guy yelling at the Caticlan airport staff as he was saying he had a 2hr connection where he had to then fly to Hong Kong and connecting to Europe and they would have to pay for his $5,000 airfare to rebook! - Yeah, don't be that guy.
A 9am arrival flight into MNL will have you leaving PP early and your hotel super-early, so you might rule that one out. Palawan is a big island - not sure how far away your resort will be from the airport. Your PR option/strategy is probably not a bad one, considering there is a later flight on 5J. Note that flights do get booked out. If the PR one looked like being delayed, you would need to be quick and a little lucky. Depending on how long you the stay is in Palawan, I may be more likely to fly back to Manlia the day before. Staying in Makati (no need to stay beside the airport), see a few of the sights in Manila (no, there are not that many), do a little last minute shopping and relax a little is not a bad way to spend the last night in the Philippines.
I don't think that the phrase "things run smoothly" and the Philippines are really meant to be used together. In the Philippines, things run on Philippines time - they sometimes just happen when they happen, for no real reason.
Oh, and I hope your PR flight to Hong Kong gets you there on time also
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