That set up looks a bit like the
dog trot houses There was some discussion about the space between the groundfloor rooms being useful for cooling rather than heating. I'm thinking you will need to take that into account when designing the spaces.
We have a similar shaped barn here and it's great for wind resistance (although on the ground not on containers) We've thought that it would make an economical home. Condensation issues and insulation of the metal skin ought to be fairly reasonable to deal with.
I found a useful site
here which has some more ideas (mostly about nissan huts which have an internal frame like our barn does.