Ex Nihilo doctrine comes from John 1:3 and Colossians 1:16, not Genesis 1. [John H. Walton, The Lost World of Adam and Eve: Genesis 2-3 and the Human Origins Debate (Downers Grove, IL.: IVP, 2015),33]
ἐν ἀρχῇ ἐποίησεν ὁ θεὸς τὸν οὐρανὸν καὶ τὴν γῆν (Gen 1:1 LXX)
πάντα δι᾽ αὐτοῦ ἐγένετο, καὶ χωρὶς αὐτοῦ ἐγένετο οὐδὲ ἕν. ὃ γέγονεν (Jn. 1:3)
ὅτι ἐν αὐτῷ ἐκτίσθη τὰ πάντα ἐν τοῖς οὐρανοῖς καὶ ἐπὶ τῆς γῆς, τὰ ὁρατὰ καὶ τὰ ἀόρατα, εἴτε θρόνοι εἴτε κυριότητες εἴτε ἀρχαὶ εἴτε ἐξουσίαι· τὰ πάντα δι᾽ αὐτοῦ καὶ εἰς αὐτὸν ἔκτισται (Col. 1:16)
According to John Walton with his idea of "functional ontology," the Genesis account was not about God creating the world ex nihilo (out of nothing), but rather it is about God forming and ordering things from what was already present, just like how the ANE creation myths narrate their tales. Astonishingly, Walton in the quote above was very direct in categorically denying that Genesis teaches creation ex nihilo in any form. Walton still holds to creation ex nihilo, except that he thinks only John 1:3 ad Colossians 1:16 teach it, but not the first few chapters of Genesis.
Walton puts forwards his interpretation by arguing that every single "creation" episode using the words normally translated "create" or "make" in Genesis 1-2, בָּרָא and עָשָׂה, "does not intrinsically pertain to material existence" (p. 29, 32). Arguing from what a word could possibly mean, as opposed to what the word is actually trying to convey, is a terrible way of doing exegesis. Be that as it may, let's overlook for the sake of argument the problems he has in translating בָּרָא and עָשָׂה. If we take Genesis 1-2 as having nothing to do with creation ex nihilo, then what are the consequences?
The first thing that we must take note is that the Jews would have held that God was not transcendent. Without a knowledge of the doctrine of creation ex nihilo, YHWH would be seen as just another tribal deity, albeit a powerful and imperialistic one. The Old Covenant Jews would have not known that God was apart from his creation since he was there molding pre-existing matter, but not creating it. The "Old Testament" god would certainly be superior to physical matter since he molded it, but he is, as far as they could have told, still very much part of the material universe. If seen from a Neo-Platonic Gnostic point of view, Walton's "Old Testament god" would be just like the Demiurge, or even the Demiurge's assistant, molding matter, while there could be other spiritual and timeless beings that were not involved in the molding of matter. Instead of saying that one believes in the "God who created the heavens and the earth," one would rather say that one believes in the "God who molded the physical heavens and the earth." If that sounds like nothing the Jews believe in, well, perhaps it is because they do not hold to Walton's interpretation of Genesis 1 and 2.
The second problem lies in Walton's exegetical principle. If the only value of words is that they COULD mean something in some context therefore, arguing from silence, it probably means that in another context, then why should we hold that John 1:3 and Colossians 1:16 teach creation ex nihilo? John 1:3 uses the Greek verb γινομαι (ginomai), which has the general meaning "to be" and is used in many places that have nothing to do with ex nihilo creation. Colossians 1:16 does use the verb root κτιζω (ktizw) which is usually translated "create" and so it seems to teach creation ex nihilo yet when one looks at the usage of the word, it is used in the LXX for example in Deuteronomy 4:32 where it said that God made (ἔκτισεν) Man. (Incidentally, the Hebrew verb used here is בָּרָא, so is בָּרָא a creation or molding verb?) It seems that therefore if one is consistent with Walton's hermeneutic, both John 1:3 and Colossians 1:16 cannot be used to support creation ex nihilo either.
The sad thing about Walton's hermeneutic is that it reduces the Bible to be just like any other ancient document of its time. When applied consistently, one cannot hold to creation ex nihilo neither can one hold to the transcendence of God. The most one can be is a panentheist with respects to God, which is better than "God" being an extremely powerful "cosmic entity" which is nonetheless constrained by the universe. he is in