The difference with soy proteins is that they actually contain estrogens...not estrogen like compounds, so when they bind to the receptor site they act just like estrogen would.
think of it like this, a cop is going around giving everyone tickets, but this cop is your buddy and can recognize your car. One day, he sees a car that looks just like yours and doesnt give it a ticket, and another day he sees a car that looks just like yours but it has a little scratch on it, so he does give it a ticket.
The 2 can both occupy the parking space, but only one of them has the same effect as your car would.
Maybe that analogy sucks, I dont know, but it seems to make sense.