The conditions needed for the fungus to grow is perfect for mold and bacteria, the reason why the fungus is not infested and destroyed is because of the ants constantly cleaning and removing contaminated fungus, if you take fungus away from the ants and leave it some where humid, it tends to mold over pretty quick.
The ventilation in massive colonies is only sufficent to remove the carbon dioxide that the masses fungus and ants produce and replace it with fresh air, not to deter mold.
In a ventilated basin the ants will be either under ground or contained in boxes with tiny holes.
So leave the ants to worry about mold and concentrate on keeping the fungus garden warmish and humid.
And most importantly get plenty of experiance with normal ants and then get experiance with Acromyrmex before you consider Atta