Peter,
First, as you recognize in your text, on a difficulty basis, lower HC numbers don't relate to hardness, but to relative difficulty (scratch vs. boggy) for match play situations (based on real average numbers from competitions, such as a flighted club championship). (That's a little conundrum, using medal play scores for a match play system, but not unreasonable.)
Second, as Jon points out, where they fall in a match play round comes into play. (E.g., no. 5 would be the first HC hole, 14 would be the second, and so on forward and backward). And
third, if I recall correctly (having not just now gone back and looked at the guidelines), the local club committee is directed to insert their own judgment into the decision as to where to award the strokes. Those are the
three factors. And difficulty, relative difficulty, that is, is only one the three. So, you just cannot say that the number one HC hole is the hardest. It's not just that simple, and it doesn't just relate to how an individual plays, but to how the great mix of players play. This is off the top of my head. For more (gory) detail, see the handicap manual (Sec. 17).
https://www.usga.org/Handicapping/handicap-manual.html#!rule-14403. Also, assume that your local club committee follows the manual's guidelines -- probably iffy on that one.
The "hardest stroke holes" (lower numbers) aren't necessarily the "hardest" holes. At my home course the second hardest hole is no. 3, a par three -- hardest in terms of average score (for scratch or plus players). Yet, it's 15 on the card. Tough par for the scratch (or plus) player, but a "relatively" easy boggy for the boggy golfer (because it's really a short par four).
Another factor, or issue, in my opinion, and this is not based on technical guideline expertise, but on experience at my club, the "relatively" numbers are set based on both players playing from the same tee, in our case, the next to back tee, as I understand it. Our number one HC hole from that tee (no. 4) is number one on account of a tough carry off the tee (both distance and fairway traps (whoops, bunkers)) -- not for the scratch, but
tough for the boggy. Then what happens when you have two boggy players, giving just one or two strokes either way, who play from
more forward tees where the carry is not much of an issue even for them? It should not be number one for them in their match, in my experience, but it is. Now I suppose you could handicap different tees differently, but I've never seen that done (except that men and women are frequently handicapped differently, even from the same tees sometimes).
Finally, keep in mind that the purpose of the HC system is simply to give the higher HC player a better chance against a lower HC player, yet being fair to the lower HC player, in match play competition. The guidelines for the assignment of stroke holes are intended to be consistent with that greater purpose.