The problem is that you can only do that so many times before people start going, "Jesus Christ, can't they just call the police or something?" Plus, then you start getting to the point where Dougworld Twilight doesn't resemble Ponyland Twilight at all if she persists in antagonizing the Dougworld heroes.
The slight difference between Dougworld Twilight and Ponyville Twilight can be what makes Pony-Twilight a hero and Doug-Twilight a villain (or more accurately, an antagonist).
Pony-Twilight is magic and she also believes in science.
Doug-Twilight is science but she refuses to believe in magic.
Dougworld itself has little-to-no magic, so it would make sense for Doug-Twilight to refuse to believe in it. She also isn't friends with the Mane Six (or Five, plus Sunset, whatever), so she doesn't get her own "Friendship is Magic" magic boost. All we know is that she scienced a couple major anomalies coming from the school, and now she wants to get to the bottom of it.
She could come into the school as a sort of Agent Scully from the X-Files. The locals tell her it was magic, but those people are naive fools, and a scientist like her knows that there's a rational explanation for everything. The illusion of magic was a carnival trick, performed as a distraction by someone sinister with something to gain, and the prime suspects in this unknown plot are the Mane Five, with special focus on Sunset Shimmer (alleged she-demon turned rock-and-roll hero).
And this whole affair started when... Twilight came to town and sang in the lunch room and tried to win a popularity contest? Nonono. You scammers picked the wrong girl's identity to steal. Twilight Sparkle will not let this mystery stand. And they even shipped her with Brad? Ew.
And they can do the "subverted expectations" thing, by having Doug-Twilight show up at school, and everyone's happy to see her, because it's Twilight, but she's not Pony-Twilight, she doesn't know these people, and she's not friends with them. She could turn the entire school against Sunset and the Mane Five, by debunking the previous two events, and raising the question "What are you girls up to? What are you hoping to accomplish by lying? Whatever it is, Twilight Sparkle is going to be the one to stop you."
If Doug-Twilight's resolve is unshakable (usually considered a positive character trait), she could be great villain, because the Mane Five are never going to back down from their claim that it was a wizard that done did it, and a pure-scientist Twilight is never going to back down from her belief that there's a rational explanation for everything, and that anyone who says otherwise is either a fool or
the real villain.
But this is just me spinning wheels in my head. The writers don't necessarily need to take this approach, and odds are, they won't. Especially not if the theme for EG3 is going to be related to the Hunger Games.