I don't think anyone believes that Go is somehow more complex than the universe it is a subset of. The point is that enumerating all cases of Go is impossible and always will be, so more sophisticated analysis is required.
Sametmax's point is that you're comparing a simple count (atoms) to a factorial (combinations of pieces). For example, it's hardly surprising that 6! is larger than 6 - factorials grow much faster than simple counts.
