I see three possible solutions for you:
1. When you want to center your model you can do this with a global transform in MED. You can do this via the menu "Object" -> "Transform Global" -> "Center".
2. You can update the entities hull by code. A simple call to
http://www.conitec.net/beta/ac_updatehull.htm should do the trick and set the hull correctly.
3. If you want to be in total control you can also set min_x, min_y, min_z, max_x, max_y and max_z. This will give you total control about the entities bounding box. The manual however recommends not to choose a box larger than the entity itself.