PHRF is, as you said, a theoretical handicapping system using dimensional specs.
The PHRF says nothing about seahandling and comfort (and little about speed)
As for "the rule"...
http://www.phrfsocal.org/INDEXED%202002%20RULES%20and%20BYLAWS.doc
Only the first 17 pages are the rule''s general description
more info on cheating the rules:
http://old.cruisingworld.com/powlphrf.htm
and the list goes on. "The Rule" is one of the most wierd systems in existance, and is constantly being changed and developed to more acuratley reflect how to handicap boats. Of course, as it is refined, boats are refined to beat the rule, which is why so many boats have bad sailing characteristics. They''re designed to beet rules, not to sail well.
When I can, I try to avoid "rule beeter" boats. (those that are built to have a handicap slower than they actualy are)
-- James