Yes I separate all my eggs, I use two layers of light grate on top of a couple of inches of perlite dampened. All of my boxes also have holes in them so the boxes aren't sealed.
I agree about water and electricity not mixing, everything is sealed off nicely with silicone that would have been exposed to humidity, the only thing that would be exposed at all to the environment in my incubator would be the circulation fans.
I also keep more than just bp's, I also have womas, spotted pythons (and soon bhps)...all of which are much more sensitive than bp eggs. They need to be kept in very high humidity, but dry and also seem to do better if the boxes they are in have some air flow through them as opposed to being sealed off. The way I run my incubator is aimed more at the australian pythons I have, but bp eggs still hatch in it just fine also.