Wow, beautiful tank set up! I'm not an expert so take with a grain of salt. In reading up on terrariums, bogs and paludariums, it seems that you can get away with doing it the ways you mentioned. I like the egg crate idea, you could use the "pet" Window screening as is it pretty heave duty compared to regular window screening. I also think you would be able to get away with any aquarium gravel - say like turface or the likes of it. I like the idea of having some water flow but then I guess it would not be a bog then? Or use your same idea and put the "box" in the back corner and have additional substrate sloping away from it? I see your challenge - so many options to choose from! I also think if the substrate is heavily planted you should be fine with the depth, though I do think having a way to do water changes would be the way to go, even it is a pipe in the back you can drop a small pump into. It will be a fun adventure, especially with such a cool tank!