Yes the condensation will go away as the substrate dries out. Also the snake isn't forced into the wet humid condition so if he wants the moisture, he goes in. When he has enough, he can come out and be back on dry substrate so he wont get scale rot. Scale rot is mostly from being stuck on nothing but wet substrate, unable to escape to dryness.
I really wouldn't worry too much, snakes will create their own hides. My little BP made a warm hide out of the bottom of her warm side humid hide. She didn't want to sit in her warm hide so she dug under the aspen under her warm side humid hide and pushed the aspen out from under it and decided this was her new warm hide. Now this morning I found her relaxing on top of the moss in her cool side humid hide. One thing though, if you use those half logs, make sure one side is pressed against the glass to help it feel more secure, preferably against the back which should have a covering on it anyways as most people cover 3 sides of a glass tank. I personally don't care for those logs and I just the plastic bowls for my dry hides and the Tupperware bowls with a hole cut in the side and a lid for humid hides.









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