Because it just makes sense! Kind of spoilers, and get ready for a long theory.

Theory:
Well, the theory is that Human Sunset used to go to Crystal Prep, but she suddenly left in the blink of an eye and no-one knows why.

The timing makes sense. One of the show creators says that the (pony) mane 6 are teenagers - probably like 17 or 18 now. Sunset is about 2-3 years older, so 19 or 20, since she 'began her studies not long before Twilight'. And it reflects into the human world, where they are a year younger than their counterparts, and in their Junior year (argue with me on this, I have proof).

Since Sunset lived in the same area as Twilight did when they were younger before meeting their friends, it would make sense for them to go to the same school (even though the areas are skewed in EqG).

She was there in the previous Friendship Games as the winner of Acadeca for Crystal Prep, part of the reason they were so strong in the games before. This is why Cinch is so disappointed when Twilight loses.

"To find a student that's like you, I've had one or maybe two, but the good ones disappear before I blink."

Right now you're probably thinking something like; "Wow Emerald, wouldn't they recognize her pony counterpart?", and I say to that, wouldn't someone figure her out eventually if there were two of her? She's quite an image now.
Twilight doesn't have to worry about this, she's there on occasion. But Sunset is technically an illegal immigrant, yet she's able to (probably) have a house, drivers license, and go to school without question. Maybe she's living under the identity of her human counterpart.

You might or might not have heard the idea that Sunset killed Human!Sunset, but it's too dark to happen in the actual show, but I believe something similar happened here that has to do with a little magic. What if either:

1. There is only one possible person in each dimension.
I believe I got this from Dr. Wolf, and while the theory isn't complete it could still make sense. This means whenever Twilight is over in the human world, something weird happens with her counterpart, only allowing one of them to exist anywhere: even in memory. (Pinkie Pie's mention of her escapes this, she's Pinkie). If they are in separate dimensions, they both exist. This happens maybe as a result of the portal, so they aren't questioned when someone goes over that maybe other people already know, to not cause a rift. This is why people don't remember Sunset, she is literally replaced in their memory. When Twilight leaves to go back to Equestra, it's as if nothing happened, Human!Twilight (and others) remember her going to Crystal Prep that day.

2. Sunset used magic to erase herself from memories
She had found her counterpart, and realized the only way to get on in this world was to literally steal her identity. Maybe a shape-shifting spell, something happened where Sunset overtook her counterpart's life. In this, Sunset still had remnants of magic once she went through the portal, though it faded over time in the nonmagical Earth.

I didn't have any more time to read this over, so if you're confused about something, jut reply and ask! It's just a theory, a pony theory.

Also, fun fact: Human Twilight's cutie mark only has the star, and not the five around it, therefore she should just technically be called Twilight and not Twilight Sparkle.