Well, here's my experience.
Upon arrival, I showed the immigrations official my round trip tickets which indicated as stay of 54 days. I asked him who I should pay for an extension. Very casually, he said, just pay the fine upon departure.
Well, I visited a few travel agencies to try to take care of the extension, but to no avail.
Upon departure, I approached immigrations with money in hand to pay a fine for staying passed 21 days allowed by the passport. The man and woman on the other side of the counter smiled at me, stamped my passport, and waved me on through. Maybe I was lucky.
You should try to take care of this through a Philippine Consulate office before departure, but if you can't, I don't think there is a need to panic. Beside the fine isn't all that much anyway.