Despite this, an alleged Coptic monophysitism has become a given in the scholarly literature. Maged S.A. Mikhail probed this question in the introduction to his 2004 dissertation, "Egypt from Late Antiquity to Early Islam: Copts, Melkites and Muslims Shaping a New Society." I don't know Greek, and can't even transliterate the Greek script he includes in his discussion, but he notes that writings from the period he studies refer to Christ as "out of two natures" instead of the "in two natures" of the Council of Chalcedon, which became the standard for western and most eastern Christianity. The idea of Coptic monophysitism comes only from the pro-Chalcedonian polemical literature. The dispute, as discussed by Mikhail, turns on whether "nature" refers to a concrete entity or a generic essence, and whether "prosopon" refers to a guise or a person. The Copts, and similar eastern churches such as the Syrian Jacobites, used "nature" in the sense of a concrete entity, and so saw the Chalcedonian formula as a form of Nestorianism, accusing its proponents of dyophysitism, a effectively splitting Christ into two beings.
Mikhail's case is convincing, but leaves some mystery as to why even Coptic scholar such as Atiya have passed on the idea that Copts are monophysites. It may be that Atiya simply wasn't that interested in doctrinal issues, being more concerned with social, cultural, and political developments. I dealt with the Copts in my master's thesis, and remember thinking that his scholarship used an anachronistic nationalism in explaining the prevalence of non-Chalcedonian views in Egypt, so he may simply have had other interests. Assuming Mikhail is write, the real explanation is linguistic differences current based on historically shaped schools of thought and usage in different parts of the Christian world.