In general, making any transformations relative to the bounding box when it comes to 3d models is just asking for issues. All adjustments should be done in relation to the origin.
As for the issues this causes:
-as
fedca wrote, due to the bounding box-based resizing method, model pivots do not align to the "container 3D Model" pivot. The adjustments in 3D Model (left/middle etc.) do not help because they are based on the bounding box...
-axis flipping is supported, but what is really needed is rotation as some software is Z-up, some is Y-up. Well, there is a rotation option in the imported file properties (not the one in 3D Model), but it still rotates around the bounding box center.