Many people use the entire end area if the piles penetrate the rock in the case of the weathered portion of rock at the surface which may be about 1m thick. Others have advocated using half of the total end area for plug formation,yet others have recommended using the net steel area for H-piles. Calls for some imagination and experience gained from past designs in similar situations.
Assuming that you had a plate at the bottom of your pile. The effect would be to allow for aa assumed uniformity of stress on your rock layer. If no plate high concentrations of stress would prevail that may have an effect on the rock capacity. For driving onto/into rock one needs to evaluate the driving stresses as piles should not be subjected to excessive stress. Limiting values are provided. This can be done using the WEAP analysis.
On the other hand if the pile was to be plugged through the overburden material and came to rest on the rock, I would probably not use the full end area.
No matter how you lookm at the problem, I would not want to use a load that exceeds the allowable structural capacity of the pile.
hence the beauty of pile design usig static analysis is the conjuring up of all these possible capacities, throwing them in a pot, and finally deciding which would be best for the witches final brew - geomagic, mumbo jumbo etc.
If you are looking for high capacity piles you may wish to look at a drilled shaft. However, this would depend on the conditions of your overburden soil.
Finally, are you providing the allowable load for the pile or is a load that is required to be taken ptrovided by the structural engineer. It make a difference sometimes.
Have fun