You'll also find that some numbers on the parts are casting numbers, and those will not show up in the EPC (cylinder heads and differentials are good examples).
The EPC is usually about 99% accurate, but it does have an occasional error. The example you cite with the coupe window regulator may or may not be an error. You don't know if a previous owner had already replaced it with the wrong part, which may have fit, but may not have worked 100% correct, or may have been modified to make it work. The brake booster may fit all models, but only in certain regions worldwide, or only with certain options. MB built cars in nearly every imaginable permutation worldwide. A good start is to set your reverse lookup feature to North America only, which will simplify things a little. And as James Dean alread mentioned, some parts have been replaced/superceded with a different, but functionally equivalent, part. So the EPC may be showing correct information, even though it may not match what you are seeing on various cars.
Bottom line: You jumped into the deep end without a lifejacket. If you don't already know MB's part number logic and general interchange, you've got a seriously steep learning curve ahead of you.
Be careful out there.