The height field seems to change the camera height if you zoom all the way in. I try to set the height value so that when you zoom in on something, the camera ends up in a place where you can see the bust. It helps in taking a screen shot of the entire creature and centering the thing on the screen. If you set it to a value equal to a human on a 15 foot creature, when you zoom in, you will be crotch-gazing.
I don't know personally if it changes bounding box height, but that would certainly explain a few things. I thought the only bounding box issues were of x-y dimensions, not Z. But I would like to know too.
Edit:
It also influences head-look, on appearances with that enabled. They will look to the height value specified. I found that out in June while working on my crystal holder placeables. I set the height level to the exact value of the nook and they looked right at it every time I interact with the object. So it can be useful when defining where to look on creature-placeables.
Edit2:
That also means that the high and low close attacks will be selected by the height of the target.