The sandals of the bare feet models I believe are to make the foot relatively consistent between "bare" feet and when you have shoes with any heel on.

When high heels like the 2B shoes get equipped, instead of offsetting the model upwards a set distance, it instead just... cuts off part of the leg. And because the rig for our characters aren't made for the feet at that angle, it deforms very, very strangely. It's why I don't use the 2B heels on my highlander. If we were to fix heels and make them work properly, we'd have to introduce a proper IK system to the animations and rigs to account for our characters having heels, which can eat a lot of resources if you have a bunch of characters on screen. IK animations tend to work better in more controlled environments compared to MMOs.

We don't have many high heels in the game anyway, and the ones that do exist aren't all that high with exceptions like the 2B boots.

That said, it would be neat if Square could think of improving on the animation system as a whole with the graphics update; better blending between animations, IK systems to properly plant our feet on the ground (with a possible heel fix), and transitions between certain animations. We don't need the actual motion physics from 1.0, but having our characters use a starting and stopping animation that blends seamlessly when we move around helps a lot for making movement feel fluid.