Dave,
I am not sure what you are asking. PHRF by its nature is a mixture of objective and subjective measures. You can ask your local committee to re-evaluate your rating, but that generally doesn't do much unless you can show evidence that there is a real issue.
As for your examples...
1) the fact that boats finish in a different order than they wind up in is a handicap system working as intended.
2) phrf is time on distance, so I am not sure what you are getting at.
The concept is that if two boats have perfect starts, sail perfect races, and have perfect equipment phrf would result in a tie regardless of their finish times.