The answer is you that you cannot stun a Scrake with Dual Flares. To stun a Scrake, your weapon needs to do at least 672 damage in one burst (shotguns can't do this because their damage is a total of many pellets hitting and battle rifles/pistols are too weak), and Flare Revolvers at best deal 160 damage. Flinching on the other hand requires at least 150 damage (which is why it can only be done with Flare Pistols used by a Rank 5 or 6 Firebug), but on Hell on Earth, you only get one Flinch to inflict on any given Scrake which can be extended maybe 2 more seconds at most.
You can however stun a Scrake with a fully charged shot from the Husk Fireball Launcher, but its charge time is not fast enough to continuously follow up with consecutive charged shots. It won't really matter if you can land all headshots with dual flares, but given the recoil of the flares and small flinch timer, that's an improbable dream made impossible since you will most likely die before succeeding.
The lesson here? Bring a Husk Fireball Launcher if you plan to Flare a Scrake to death, but if there is a Sharpshooter with the Xbow or LAR, let them kill the Scrake since flaring a Scrake wastes more of your ammo than a Sharpshooter would waste in killing the Scrake.