The setting "bitwise" in the Enzo config system refers to ensuring sequential pairwise averaging in the potential solve, when computing boundary conditions. While this does reduce variance in the solve from timestep to timestep, it is not (necessarily) a method of ensuring bitwise identicality; compiler variance is in my tests the dominant factor in ensuring identicality. I implemented this functionality.
In recent tests, I have found that for nested grid simulations, turning this off sped up calculations by more than an order of magnitude.
I am issuing this pull request to leave the option in, but to disable it by default. I believe this is safe and appropriate, and it should pay off for anyone doing AMR calculations.