If the time on distance version of PHRF is being used, then in stronger winds, the faster boats are going to have an advantage over slower boats, and vice versa in lighter winds. That's just the way the math works - nothing to do with the characteristics of the boats. If a race is 10% faster than average, then an Ensign with a 262 rating racing a J24 with a 170 rating will have a abs((262-170)/1.1 - (262-170)) = 8 second per mile disadvantage. That's why time on time is fairer.
I've looked into handicap systems pretty extensively because I did the scoring at CYC for our holiday handicap races and noticed that the different boats were winning when we did a time on distace pursuit race versus a regular race where we traditionally used time on time. I believe that over time the PHRF ratings have lost their relationship to actual boat speed because PHRF committees just focus on the delta between boats and because PHRF ratings have an offset built in which sort of hides the rated boat speed (USS says that PHRF + 550 should equal a boat's VMG in seconds per mile, but this isn't well known or given a lot of attention, and it's become inaccurate for many boats).
ORC rates a J24 at 795.3 seconds per mile. ORR rates it at 794.7. With rounding, both of these translate to a VMG of 3600/795.3 = 4.53 knots. ORC doesn't have an Ensign rating, but ORR rates an Ensign at 913 spm (3.94 knots VMG). So according to these systems, which are pretty high-tech, there should be a difference of 118 seconds between a J24 and an Ensign. A common J24 PHRF rating is 170. So that means an Ensign wquld be 288. That would work for just Ensigns and J24s racing each other. But PHRF needs to have a consistent relationship across fleets between boat speed and the rating for the math to work - i.e., there has to be some x where PHRF + x = VMG in spm. So if we stick with a 550 offsett, the J24 rating should be something like 245, and the Ensign rating should be 363. Or a different offset needs to be picked and certain boats adjusted if their VMG is out of whack. Or just get rid of the offset and state the handicap in spm to avoid confusion.