Hrm... Well, the compression tool should compress the file exactly the same every time, it's not like an algorithm that varies or anything. As long as the duplicate meshes are all compressed, they should still have the same checksum IF the meshes are each in standalone files. I can understand that the checksums would be different if one mesh was bundled in the same package as a recolor and then the original, standalone mesh package would have a different checksum, but otherwise I don't know why they'd have a different checksum. Unless, of course, the Bodyshop changes the meshes when it bundles them in some way or otherwise screws things up.
Sounds like the problem though is especially bad for Mac users as they don't HAVE another way to install Sims2Packs, they can ONLY use the installer that comes with the game. And, assuming that Aspyr uses the same Bodyshop code, their Bodyshop probably has this same stupid bug and they have no way to clean anything they create...
Stupid EAxis.