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Yes moisture is a big issue with these types of containers. I have one that I have used for several years as a workshop/storage shed. With good seals these things are dang near air tight and when they heat up in the sun the condensate horribly. You can put a roof vent in them and relieve this problem but since you are looking to use it as a bug out home you will want to figure out a way to filter the air coming into container.

Also look at the weight ratings for stacking them. It will give you an idea of how much weight the walls and roof can support. Depending on how much concrete and split rock you are looking to use on the walls they may not hold that much weight, especially if you start cutting doors and windows into them.