The alterations are not actually important in discrediting Antiquities of the Jews as an eyewitness account of Jesus, or the historical Jesus (or whatever it’s being used for), for the simple reason that Josephus discusses God's creation of the earth, Adam & Eve, Noah & the flood, the Tower of Babel, the 10 Plagues, and the parting of the sea, etc.
This is, clearly, not eyewitness reporting, nor is it relating to historical events void of religion, but mostly historical events according to religion:
"Now I have undertaken the present work, as thinking it will appear to all the Greeks worthy of their study; for it will contain all our antiquities, and the constitution of our government, [**]as interpreted out of the Hebrew Scriptures[**]." "I shall now betake myself to the history before me, after I have first mentioned what Moses says of the creation of the world, which I find [**]described in the sacred books[**] after the manner following."
- Antiquities of the Jews -- Preface