RE: Engine Pod - how much support?
The balance tabs on the tail surfaces look fine to me. It's as much about the area forward to area behind as it is the chords.
However looking at the engine pod and nose side area I'd suggest some additional poetic license be taken in increasing the vertical tail area by about 20% over what it currently is. As it sits I think you're in for trouble in terms of spiral instability and possible unwanted snap rolling.
Using the "scale" struts would definetly make things more complex. Just because of the fact that I'm stubborn I'd go with it but I'd make the wing center fixed to the model along with the engine pod and make the wing panels fit onto the center section.
And while the drawing doesn't show it you'll want to add about 3 to 4 degrees of upthrust to the engine to compensate for the very high thrust line. Study some other high thrust line flying boats to see what I mean.
The bit under the tail could be fattened up and lengthened without hurting the looks. That would help stabilize the tail nicely. I'd still use functional bracing struts though.
And there's no water rudder. You'll likely want one of those.
Many (most?) of the planes in the movie were scale. THat's a big part of what impressed me so much. Just Porco's racer was a work of fiction but even then it's firmly rooted in Savoia Marchetti design school.