if you dig into this thread (nikon specific) and read between the lines you'll probably come to the conclusion that:
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1) there are a lot of details about the implementation of the battery that the camera has good reason to care about
2) not all 3rd party batteries implement these things
so, sure, some batteries may be just as good, but, at least in the case of recent nikon batteries:
a) it seems likely there are valid reasons for the camera to reject some 3rd party batteries
b) if the camera did a good enough job replicating the oem battery, it might not be rejected
c) the juice probably isn't worth the squeeze