A possible scenario could be that caves such as Pen Park Hole could have originally formed at depth by ascending thermal waters charged with CO2; these theoretically would dissolve along lines of weakness but create only small cavities initially. Indications of these would be calcite-filled vughs and evidence of altered rock. At a later time uplift would have raised the caves where normal phreatic solution could take place, enlarging the existing voids.
How does that sound?