Flamethrower is more reliable than Focus Blast for taking on most Steel types, such as Magnezone or Aegislash, has a chance of burning targets which is more useful if they switch in a Dragonite or Zygarde or Azumarill or whatever, and... well, Flamethrower doesn't miss. Most Noivern are Choiced and will have to successfully anticipate the switch-in of Tyranitar, or else be unable to take it down, at risk from Return and at risk from Pursuit should they decide to switch. Aegislash in particular 100% walls Noivern if it runs Focus Blast over Flamethrower, and even with how little it gets out of the meta is still a powerful, flexible Pokemon.
Overall it's fairly redundant with Aerilated Boomburst, what with both being effective on Grass and Bug and resisted by Rock, while Focus Blast provides coverage on Rock and also provide's Fire's coverage on Steel, so there's definitely arguments to be made for running Focus Blast over Flamethrower, but it's not actually a clear-cut improvement over Flamethrower.
Your numbers are also misleading anyway, because they only hold up if you actually assume Choice Specs. I see Scarf a lot, and for Scarf Noivern Flamethrower is more reliable on both Mega Scizor and Ferrothorn over Boomburst, vs Focus Blast being inferior against both of them. I've also seen Sashed Noivern, Life Orb Noivern (For whom Flamethrower always OHKOs Mega Scizor and Boomburst only usually OHKOs it), and I think even Sharp Beak Noivern.
