Periodization involves simplification and is always up for debate; it should be thought of as a helpful guide, rather than hard and fast divisions. Traditionally, Egyptologists have tended to consider Alexander's conquest as the chronological terminus of their field, deeming the preceding few centuries termed the "late period." There's really no good reason for this, however. Egyptian language and culture flourished in the Greco-Roman period. Foreign conquest cannot be used to mark the division either because Egypt was often ruled by foreigners, including the Achaemenid Persians in the "late period." Since Greco-Roman Egypt was generally left to classical historians trained in Greek and Latin, there has long been a neglect of the voluminous Egyptian-language evidence from these periods, which is now being rectified. Egyptologists, in turn, have come to realize that they have much to gain from the relatively well-documented later periods.

To answer your question, I think that it's more meaningful to include the Greco-Roman period in one's conception of ancient Egypt and this appears to be becoming the norm. The Oxford History of Ancient Egypt (ed. Shaw, 2000), for example, concludes with chapters on the Ptolemaic and Roman periods.