How do I re-wire my Airstream Fusebox so as to follow best practices?
Your photo suggests one of two possibilities - either:


Whoever designed this had limited electrical knowledge, or
The two-legged battery fuses were a simple and inexpensive way to provide removable isolation links that allow either or both batteries to be fully isolated. 


My guess is that it's probably a combination of both of the above, since it's only necessary to isolate one side of the battery. Your chosen selector switch looks fine, and includes a position that isolates the +ve leg of both batteries, so that's taken care of.

You only need to fuse one side of the circuit. Your first diagram looks Ok, with a couple of changes: I would fuse the positive battery supplies not negative, as that's usually simpler re wiring, and more consistent with what the next owner would expect.

I tend to be overly cautious with these high-current sources - I'd fuse each battery positive separately, and before the selector switch. That would protect against one battery undergoing some form of internal mechanical failure and going low resistance when connected in dual mode. This could happen with older batteries, but very unlikely with modern ones. 

And if every circuit is properly fused, the battery fuses are really just protecting against an accident with a screwdriver or similar, when working on this panel.