Well, honestly I'm not sure. You would think that by having two corners open 24/7 that you would have some air exchange inside the tank. You know, another option is to treat the algae you have now with some hydrogen peroxide. Whenever I am doing a dry start, I try not to have any standing water in the tank. I use a turkey baster to remove any standing water that may accumulate over time. Another thing to consider is that you could just let the algae go for now and right before you flood the tank you could dose hydrogen peroxide and work over the rocks with a toothbrush. I believe that alot of the algae on the rocks will come off that way when you flood it.
Maybe some one else with more experience will chime in soon.