The logic is this: If Padme does marry Bail Organa, then Leia would never have any "mother" in her life other than Padme. So when she speaks to Luke of her mother, it could only be Padme. We know that Leia will come to see Bail as her father. Maybe she will really believe he is her biological father. So she must consider Bail's wife to be her mother. On the other hand...I forgot that maybe Luke said "your real mother..." If that's the case, then she knows she's adopted and she's speaking of her real mother.