@ZarathustraReborn,
The Testimunium Flavinium is not the only place where Jesus is mentioned in the Antiquities. There's also a mention of the death of his brother James in Jerusalem. And even if the testimunium was evidently redacted, many scolars think that it was not
added in its entirity. Rather, a nucleus was expanded upon... At a bare minimum, that's a possibility.
The Talmud also mention Jesus extensively and quite negatively. Written 2 or 3 centuries after his death, you would assume that if there were any reason to believe he was a fictional character, the good rabbis would have used this argument against him.
Why focus only on Jesus though? Did John the Baptist exist? Did Zarathustra? Did Hillel? Did Shakespear? Did thousands and thousands of historical characters mentioned here or there in passing in one text or another actually exist? A huge field of enquiry is open to all the conspiration theorists. Why pick up only on poor baby Jesus?