I'm an Arabist, so perhaps a French expert could answer your first bullet point on why France invaded Egypt with greater expertise, but the first point appears to me to be nonsense and the second and third points I can say, definitively, are nonsense.

First Bullet Point

To briefly touch on the first point, at the time of the invasion, the Mamluks in Egypt had reasserted their power and were governing as a de facto independent state despite Ottoman suzerainty. As for new governors, as I said, a French expert may be able to answer as to the French rationale, but in the context of actual Egyptian governance invading because a new governor was on the way would be nonsense. The Ottomans appointed or were forced to appoint new governors to Egypt constantly: https://en.wikipedia.org/wiki/List_of_Ottoman_governors_of_Egypt

As you can see, before the invasion the Ottomans appointed a new governor about once a year. Many of the governors on that list met violent ends at the hands of the Mamluks, some after only a matter of a few months. Moreover the governors did not wield much in the way of power anyways, again, because the Mamluks maintained real control until Napoleon's invasion and, subsequently, the rule of Muhammad Ali Pasha.

I've read publications by Napoleon made in Egypt to the effect that he was liberating the Egyptian people from the Mamluks but I'm unfamiliar with any faction, either the Mamluks or the Ottomans, inviting him into the country, and indeed, both parties fought against him.

In practical terms it's my understanding that Napoleon and the directory were far more motivated by the geo-strategic advantages of controlling Egypt, particularly access to the Red Sea and, by extension, a direct route to the Persian Gulf and India that could threaten Britain's empire there and/or gain them their own French one.

Second Bullet Point

This is basically ludicrous. The reason why the French invasion of Egypt is often taken as the starting point for "modern" Middle East history is in large because it marks so clearly the point at which we can definitively say that at least one European country (France) had assumed a position of near total technological dominance over the military powers of the Middle East.

Prior to Napoleon's invasion there is a strong case to be made (and one that I have made repeatedly in this sub, following the arguments of, for example, John Darwin) for much of the preceding centuries that the Ottomans were at parity or near-parity technologically with Europe.

Napoleon's invasion of Egypt demolished that illusion, and both Egypt and the Ottomans would spend the next century instituting civil, military, technological, political and administrative reforms to try to catch up and "modernize" as exemplified by the "tanzimat" (i.e. reforms) in the Ottoman era and the reform programs of Muhammad Ali and his successors in Egypt.

The military example of this was demonstrated at the Battle of the Pyramids. A quick glance at the casualty figures tells the story.

Aside from mere feat of arms, the French brought the first printing press to Egypt. (Although, as an aside, it's my understanding that the propaganda they produced was translated horribly, and in a society whose elite was based in part on years of study of classical Arabic grammar this significantly undermined Napoleon's authority).

I'm struggling to think of an example where the Egyptians would have had superior technology. Tocqueville writes of the French occupation of Algeria half a century later that the Algerians had higher rates of literacy than the French themselves and this was reversed by French efforts to spread the light of civilization, as it were. He doesn't cite a source for those estimates, but in the case of Algeria it doesn't seem unreasonable to me. For Egypt I would strongly doubt that that was the case.

The Ottomans would in many cases have had access to the same technology, but as with Napoleon's defeats of European powers the French revolution was as much a question of administrative, political, strategic and tactical innovation as it was of strictly technological change. Both the Ottomans and the Egyptians, as with many European powers, would struggle to emulate the French example of the virtuous circle whereby popular support enables administrative reforms enables higher tax revenues enables the levee en masse whose victories partly feed back into more popular support. The Egyptians were more successful at understanding that you had to have a modern state to have a modern army. The Ottomans tried to just introduce the technology and the military changes and this contributed significantly to the victories of Egypt in the Ottoman-Egyptian wars over the next half century. (There are other reasons for this, the Ottomans left the Jannisarries as an entrenched class where as Muhammad Ali Pasha slaughtered their Egyptian equivalents, the Mamluks and thus had a free hand to reform the state and the army to his will.)

Third Point

A French expert may be able to discuss more what this group intended to study and whether there was any conception that the findings of the scientific expedition might have had practical uses, but in the context of the second point about superior technology I can also say that this is simply incorrect.

Have a quick glance at the volumes of the Description de'Egypte that the expedition produced: https://en.wikipedia.org/wiki/Description_de_l%27%C3%89gypte

Their 24 volumes are almost entirely dedicated to "what they saw" in the form of botanical, geological, and zoological observations combined with archaeological and historical observation and assessment.

Again, it's possible that there was some idea out there that they could bring back something useful to France but that is not at all in line with what I've read about the expedition and demonstrably did not happen based on what they actually found and published.

TL;DR unless something has been seriously miscommunicated your new professor is full of it or needs to step up with examples and sources.

Sources: Oh, where to begin? In a single volume history of the region I always recommend Eugene Rogan's The Arabs: A History and will provide important context.

As I alluded to John Darwin's After Tamerlane is a very useful reappraisal of the relative balance of powers between European non-European states.

There are several dedicated histories of Egypt that are quite good. P.J. Vatikiotis' From Muhammad Ali to Mubarak might be a good first port of call (despite the title, it too starts with Napoleon's invasion). On administrative/cultural/technological reform, I hate the style of it (the author follow Foucoult) but Mitchell's Colonizing Egypt on the eponymous subject goes into the state of daily life and technological changes in Egypt from Napoleon onwards.