According to Dr. Zahi Harwass there are just 4 female Pharaohs in Egypt's long history. In his book, Silent Images Women in Pharaonic Egypt, Harry N. Abrams Inc, Publishers pg 35. He states "throughout the long period of Egyptian history only four women became rulers...which illustrates how alien this was to Egyptian culture."
Queens Nitokerty(6th Dynasty), Sobekneferu(12th Dynasty), Hatshepsut(18th Dynasty) and Tausret(19th Dynasty) are the four women. He admits to having ruled Egypt in their own right. He mentions the 1st Dynasty Queen Merneith (pg 31) as possibly ruling in her own right but states that information from this early period is too scanty to provide clear evidence. While Toby A.H. Wilkinson in Early Dynastic Egypt declares her to have ruled as Co-regent in her son's name.
Dr. Harwass writes (pg 35) that what makes Hatshepsut so different from the other female Pharaohs. Was that she took the throne in an apparently peaceful prosperous period in the middle of a thriving dynasty. This is the "anomaly" his word for Hatshepsut's rule and sets her apart from the other queens who came to their throne at the end of their dynasties during times of crisis and upheavels. He makes clear that the "anomaly" of Hatshepsut was never repeated in Egygptian history.
As for the Ptolomy Queens, being Greek not Egyptian. The concept of Queen was understood by them if not their Egyptian subjects. Ptolomy Kings and Queens ruled in and from Alexandria which controlled all of Egypt. Very few of the Ptolomies were acutally crowned as Pharaoh of Egypt. To do so meant being less Greek and more Egyptian than most preferred. Cleopatra VII was one of the few Ptolomies who was Pharaoh and Queen. Cleopatra VII spoke and wrote native Egyptian she was one of the few Ptolomies to do so.