Short answer: no, you aren't wrong to assume that the article is flawed by the fact that it solely focuses its efforts on contorted theories and without any actual evidence.

Long Answer: There isn't any credible evidence there was any Exodus of Jewish slaves into or out of Egypt, let alone on the scale they cite. They claim the Jews were enslaved for over 400 years ("At the end of the 430 years, to the very day, all the LORD's divisions left Egypt." Exodus 12:41) and that at least 600,000 men, plus women and children all left at at the same time in a great migration (Exodus 12:31). If we look outside the bible, it's interesting that there is very little mention of the Egyptians anywhere outside the bible until the 12th century bce. Historian Eric Kline actually discusses part of this in his book about the collapse of the Bronze Age (cited below), and he mentions Merneptah, who is the first non-Isrealite to mention the Jewish people at all.

Merneptah is perhaps best known to students of the ancient Near East as the Egyptian pharaoh who first uses the term “Israel,” in an inscription dating to this same year (1207 BC). This inscription is the earliest occurrence of the name Israel outside the Bible. In the Pharaonic inscription, the name—written with a special sign to indicate that it is a people rather than just a place— appears in a brief description of a campaign to the region of Canaan, where the people whom he calls “Israel” were located. (Source: Cline, Eric H. (2014-03-23). 1177 B.C.: The Year Civilization Collapsed (Turning Points in Ancient History) Princeton University Press. (pp. 6-7))

Now what's the significance of posting this excerpt? It's to show that the Jewish people weren't known or much cared for during this time period and that they are not even mentioned until well after the Exodus would have supposedly happened.

It's also worth noting that during the new kingdom of ancient egypt, the entire area near present day Palestine and Israel, which was known as the Levant were all Vassels of Egypt, for hundreds of years… We have no evidence of any group calling themselves Isralites or Hebrews or anything of that effect until 1207 (as Cline points out) and we do have hundreds of documents (many of them letters) between all the other kings and tribal leaders who did occupy this area during these centuries. This isn’t to say that Jews weren’t living in this area during this time period, it just suggests that they weren’t relevant or numerous enough for the Egyptians to care about let alone enslave.

That said, I also want to address one key piece of this document that I have the biggest issue with:

Ninety-nine percent of the papyri produced there during the period in question have been lost, and none whatsoever has survived from the eastern Nile delta, the region where the Torah claims the Hebrew slaves resided.Instead, we have to rely on monumental inscriptions, which, being mainly reports to the gods about royal achievements, are far from complete or reliable as historical records. They are more akin to modern-day résumés, and just as conspicuous for their failure to note setbacks of any kind.

First, they are no credible scholars that I have ever seen give this estimate of 91% given anywhere, nor do they cite such a number. Even John Baines Oxford Scholar who has studied and written about Egypt more than any other person on the planet has never given an estimate for how much we don't have. Yes, it's considerable, but to give a hard number, that seems strange.

I also want to address the fact that while they discuss pieces of information such as monumental inscriptions as being a "modern-day resumes" they leave out the fact that we get most of our information about Egypt from a variety of other sources, including Annals (inscribed chronologies of major events) Archeological evidence, Artistic Evidence, and Textual Evidence. The article fails to fully understand how we understand our concepts of Egypt, and with some small exceptions, we have no problem fully piecing together the history of Egypt from a millennia before it was even considered a civilization (about 4,000 bce) all throughout its time as a Vassal to Rome. If anything was ever uncovered which showed significant proof of a mass incarceration of any sect of Judaism was in Egypt for nearly half a millennia and then wondered around the desert for 40 years, we would have found it by now.

Hope this helps.