Only a fool believes that “everything comes from nothing.”
That's a rather harsh self-assessment of yourself and fellow creationists. “everything comes from nothing.” is the basis of the storyline from your favourite fable. Hopefully seeing the foolishness, and acknowledging the issue, is the first step to seeking the truth.
It looks as though you completely missed the point. With regard to substance, to "create" is to make something from nothing. But, TF49 did not speak of "making" a substance - not at all.
Substance - the created. Source - the Creator.
He said "comes from" - a statement about source, not substance. The point being that God is the source.