Well here are some canon comments to put this in perspective…
 
Applejack about Twilight “She’s awfully strong for such a small pony.” (implication that she’s a small unicorn, if not the smallest of the group)
 
Rainbow Dash about Applejack “Looks like this pegasus can pitch better then this work horse.”  
(implication that AJ is the biggest of them, bigger then RD, sense the term horse is used to describe ponies of huge size)
 
Rarity about RD “Even though she’s built just like a tank.” (implication that regardless of her size, her body is absolutely ripped, which is natural)
 
So really, since height has never been RD’s biggest attribute, and Twilight isn’t remotely as tall as a natural Alicorn, I don’t see this as a big issue. Twilight being a princess in certain episodes have FAR more glaring problems then 6 inches or so on Twilight.

@Dragonmage  
Powerhouse? wouldn’t that suggest that she takes on enemies without gaining momentum first?

@Kj2  
Meant to be a response for @Dragonmage

Actually AJ is the powerhouse, Dash is the faster/aerodynamic so ‘the smaller the better(?)’

@Villain Pony  
^ Considering she’s the powerhouse of the group, I’d imagine she’s more larger than some of the others.

I always imagined Dash being the shortest of the mane six.

So she’s standing on the tips of her fingertips?

Twilight: Bitch i’m tall  
Rainbow Dash: i can fly you can’t

Probably better to use AJ; Rainbow would be doing this flying. :/

Twi, she mad!

to small