This is just my opinion & experience. I'm about 5'3" with an inseam of 30" to 31". No seat modification. I have the, E46 on my S'Wing. I know it's there, even when it's empty, but have had no problems. But before I purchased it, I would use a fully loaded duffel bag strapped to the seat. To me, no matter what you get you're going to change the balance of the bike, be it high or low. You'll know it's there, you just have to adjust to it.
If you're still not flat footing your scoot you may want to try & find a pair of boots with a thicker sole. Really...........it's not that bad having one, you will get use to it & if you were to use saddle bags too, it may help out with balancing it out and give you even more room for goodies when you take a trip. Hope this helps.