It's called a hitbox and it's something that won't ever change lol. With XIV they actually tried to fix it, but as usual the community bitched about not being able to run through enemies (ironic huh?) so they removed collision detection.

Developers can only do so much to try to fix it but as long as big entities exist there will always be weird problems like this, since they can make the hitbox universal like some enemies in XI (Hydra for example) but the main hitbox will always be in the center.

As for the Amphiptere screenshot look at how he's also clipped into the ground, which changes his stance which makes them get even more in your face or not lol. But as said, as long as there's large enemies, always expect there to be graphical hangups like this, especially if people will continue to complain about collision detection >.>