In my opinion, there are too many constants and predefined variables for it to not be premade at least in some shape or form. For starters, the most obvious place to look is the periodic table. Elements would have to pre-date the beginning of the universe.
Then there’s gravity, light, and potentially the universal concept of natural selection. The most interesting of which is gravity, since it’s the glue which holds everything together.
I haven’t looked at it in detail, but the Matrix comparison is likely just a relatable catch phrase to get the average Joe pick up the book.