coordinate transformations upon import / export (ply and obj format)

I am experimenting with import (and export) using ply and obj format. I am rather confused that blender seems to implement additional coordinate transformations upon import / export:

When exporting an object to the ply or obj format, the vertex coordinates in the ply or obj file are rotated by -90 degrees about the y axis as compared with the original coordinates displayed in blender. When importing an object from an obj file the object properties of the imported object include the inverse transformation (rotation about the y axis by +90 degrees). Of course, if the obj file was not created by blender, this extra rotation is rather annoying.

When importing an object from a ply file, no such rotation is applied to the vertex coordinates. So blender’s orientation of the object agrees with the orientation of the object in the ply file. Yet this also implies that exporting an object to ply (thus rotating it by -90 degrees) and subsequently re-importing it rotates the object by -90 degrees.

All this applies to blender 2.62 (default configuration). Can this behaviour somehow be switched off (i.e., no rotations upon import / export)? What am I missing here?

I found a thread “Add transformation before export” where the OP apparently had similar difficulties. Yet no solution to this problem were posted in this forum.