If this universe is completely reductionistic, which a simulation probably would be, then your "actual thoughts" (and the existence of trees, etc.) are logical implications of the configuration. Does an entity with logical uncertainty still count as omniscient? But then we've gotten into definitions again.

I still don't know whether you, personally, think a deistic god implies that one or more religions is true. It doesn't particularly matter, though. Your original point that the answer to the god question depends on the answer to the simulation question is a good one.