True, but you'd also be ignoring Darm's self-destructive nature. Notice how Darm can't even survive two of its own Flare Blitz's and one hit from the enemy Throh. That's pretty damn bad. Meanwhile, Scraggy has ridiculous bulk; the complete opposite of Darm.Trainers rarely run at least 3 pokemon around the 4th gym (i'm pretty sure for instance, the only trainers to do so are Burgh and Elesa, and a bunch of derps carrying around the monkeys in the stadium). Moxie Scraggy's damage leads after 2 kills are insignificant early on because this damage lead, for whatever it's worth, only exists for a couple of specific trainers. Even rare are trainers running 6 Pokemon that allows Scrafty to maximise the usage of Moxie (Iris, Ghetsis, Colress... any more...?). Trainers with 3 Pokemon are more common towards the latter end of the game, so the point made is that Scrafty only barely outdamages Darm after two kills, and cleanly does after three. By then, most of the opponent's party would've been dead already, leaving Scrafty's advantages moot. On the other hand, Darm is basically +2 Scrafty from the get go, and is fast enough to brutally murder anything that doesn't resist fire or doesn't have any semblance of decent bulk. From your Darm VS. Throh example, it's clear that something as bulky as Throh is very nearly OHKO'd. Something frailer will not live a Flare Blitz to strike back a weakened Darmanitan.
The advantages are pretty clear to me. Darmanitan > Scrafty. High Scrafty.
You also talk about murdering anything that doesn't resist Fire...that's four different types that its completely ineffective against. Scraggy on the other hand has perfect coverage.
I really see it as a toss-up.