I feel that the cherry picked fighter situation is just that. How many 45th+ level fighters are there in a chapter?
Here's a better solution. Take your 45th level fighter with their DA and slayer/reaver and peg them with a web. Done. So the issue is magic items, pull em. That fighter, if they swing for 100's will still be a 2 spell kill.
In your scenario, in stead of adding body, add lives to the npc.
Except that only solves part of the problem.
The second part of the problem has to do with disparity between PCs. Take any two casters (ignoring wands and high magic for a moment) and put them in a fight together. As long as the first one is at least 7th level, that caster has access to every single spell that the 40th level caster next to them has. The total number is smaller, which means they run out of steam much quicker in the long run, but in any single fight that caster can contribute equally if they are willing to go all out. Heck, even a 5th level caster basically has the same set of options (since low and medium level spells tend to be the bread and butter spells of the game).
A 7th level fighter, though, is going to feel all but useless in that same situation. Even with complete focus on profs, they swing at best 6 damage with sword and board, compared to the 40th level fighter who can be nearly 5 times that number. Drop the fighter down to 5th and they feel even more useless, even compared to a 20th level fighter (the average for many chapters).
Scaling back profs so that the difference between low level fighters and average level fighters (roughly 20) is less extreme helps make all PCs feel more useful. The disparity will never fully disappear, but it helps if we can, as a game, make it feel less daunting.
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My current instinct is that making fighter one-shot skills more enticing will help a lot. If Mettle cost 10 body points to guard instead of 10 seconds of time, it would definitely jump near the top of my "must-buy" list. Similarly, if Resolute was a skill that you spent when you went from 0 or -1 body to positive body (including after waking up a minute after first aid) to immediately heal an extra 10 body (maybe multiple could be spent at once), it would be much more enticing in my mind. Add maybe one more good fighter skill and I think proficiency purchases would drop notably.
Furthermore, my other current instinct is that maybe we should have a rule, across the board, where any skill costs double on your 5th or later purchase of it. That would slow down profs and backstab bloat AND also slow down casting bloat. Formal levels and crafting could have an exception that they don't double until the 11th or later purchase. I'm kinda spitballing, but this slows down progression overall without preventing people from focusing or putting an arbitrary hard cap on the game. It also would probably mean that we would no longer need such harsh pre-reqs for fighter and rogue skills.
-MS
P.S. - Magic items that duplicate profs / double damage also need to be nerfed HARD