Googling "bake a binary" returns five hits, but only one of them is a site that isn't blocked with a security warning. That piece was written by a guy who uses the phrase "baking a binary" to describe his approach to embedding a binary file "as a const char array in a C/C++ header."
A search for "baking a binary" returns three hits, all to the author mentioned above.
There's no telling where Flynt/Wu picked up the phrase or what he means when when he uses it. (OK, that last part is not quite true. What he means is: "Here's some nonsensical babbling that will help cement my reputation as a software engineer among those who have no idea whatsoever how computers work. It is the I-know-software equivalent of his I-know-history sperging about all the people who died of dysentery on the Boston-to-San-Francisco wagon trains in 1780.)