DHX made their own mods, along with using some proprietary ones, pic related. Only a few effects scripts showed up in the leaks, so I don’t know exactly what they used, but it does confirm that they were modifying flash.  
I suspected that they were doing this because the symbol trees are too complicated to have been done manually. The Double Rainboom puppets use symbol swaps to change character rotations, while DHX put all the rotation frames at the very end of the character’s timeline and you can see this by extending the timeline of any animation (example here)  
These puppets are meant to interact with scripts and mods. The layer names (such as “//sync” on the heads) are even indicative of this.  
The reason MLP looks as good as it does despite being made with flash is because DHX heavily modified it. Things like walk cycles are saved outside of the main puppets and are only imported when needed. Even the S9 faces were the result of mods.