Think of the process fabrication whenever possible in understanding layout.
POLY is always grade A photomask, meaning the one of the highest ranking in photomask fabrication, same as some metals. Diffusion is instead not, also, it is formed from doping concentration by ion implantation, which is typically not very good in control compared with poly, so the profile is not as good as POLY. PP cap is formed from two POLY layers, as a result, the oxide built in between is more uniform that the oxide formed from gate to diffusion. However, as gate oxide tends to reduce with decreasing technology, so MOS cap tends to be much larger than PP cap, some multiples to PP cap is not uncommon.
However, MOS cap has to be biased with a gate voltage such that the MOS cap is being constant, which is also a major factor for its value being varied from PVT.
Remember there is voltage and temperature effect from PP cap as well