A boat does not have to have a valid GYA PHRF Certificate. If the R/C gives the boat a temporary PHRF Handicap then no they are not subject to the 6 second hit and the rating can not be protested.

Quick read through the NOR would have answered your question.

This is a PHRF regatta. All boats with a GYA PHRF certificate, including X-PHRF and multi-hull certificates, are encouraged to race. A temporary handicap will be assigned by the race committee to boats without a PHRF certificate; however, an application for a permanent rating must be made to the GYA within two weeks or a 6 second penalty will apply. Temporary handicaps are not subject to protest.

Now which boat are your referencing so the RC can be made aware of the issue.