Yes, although there's an asymmetry here. If A says "I assume God exists", and B says "I assume God does NOT exist", if God is not self-evident or logically necessary, B can at *least* appeal to the non-self-evidence of God. In terms of self-evidence or logical necessity, there is no God -- it's something that would be argued for as a conclusion.
Pretty much the same as someone who presupposes no god, makes no god a presupposition without evidence and arguments, but just as a starting point?
B's proposition is illicit, too. Even if God is not self-evident, there's no necessity for a proposition like "God does NOT exist". This too can and should be denied as an axiom. As a matter of necessity, there is not disposition either way, at the very start. We begin in a state of not knowing, and propositions like that are matters to take up via investigation and contemplation.
The scientific method seeks natural explanations for natural phenomena. That means that metaphysical propositions like "God designed the universe" or "The universe just popped into existence uncaused" or "The universe is cyclically infinite" are beyond the scope of science; it has nothing to say on the matter, because it is methodologically bound to natural explananda. This means that neither atheist nor theist gets any relief or any refutation from science on the matter of how the universe came to be.
The singular difference here is the fact that logic and science give weighty evidence for a Ã¢â‚¬Å“Causal AgentÃ¢â‚¬Â, Ã¢â‚¬Å“Prime MoverÃ¢â‚¬Â of all the design and life we see around us in this universeÃ¢â‚¬Â¦. We choose to call Him God because He is evidenced in these observations. Evolutionists worship an unintelligent being they wish to call Ã¢â‚¬Å“NatureÃ¢â‚¬Â or Ã¢â‚¬Å“Random ChanceÃ¢â‚¬Â so as to avoid the sum total of the whole.
Logic has to do with form and structure. Without being appealed to experience, it doesn't provide real knowledge. "Brute logic" doesn't tell us anything about the reality (other than, if you want to really be fastidious, that one exists, necessarily as a condition for thinking logically). Neither logic nor science have a path we can identity to building and verifying metaphysical knowledge about questions concerning the (non)existence of God, or the (non)cause of the universe.