Steven Universe - Ian explains a thing

I had no idea how impactful her hair was on how we perceived her size.

Well, even though they are shapeshifters, gems have been shown to have a 'base' model whenever they regenerate. With amethyst's birth defect essentially being dwarfism, she cant 'force' her model to grow taller, but she can shapeshift into the Purple Puma, who fits a bit more into what she was originally supposed to look like, minus the chest hair.