Alex, I suspect your suggestion is what I had in mind when I mentioned "nesting" the secondary and primary frames... It's the only way I can see reducing the overall thickness of the hull while accommodating the frame members.
SicOne, as for excluding the hull frame from the thickness, I don't think you can rightly do that, but I'm not sure. That is, at least the thickness of the secondary frame needs to be considered, as I suspect it's members would be generally less than 5m o.c.
Where the primary frame's major members are at 25 m intervals (82 feet), I would certainly exclude them (nesting allows for that), but I still have the primary frame's minor members at 5 m intervals (16.4 feet).
So, at a minimum, I'd argue you'd have the thickness of the minor members from the primary frame, the major member thickness in the secondary frame, the connecting rods between them, and the 12" of hull.
So far as beam dimensions go, I see a variety of approaches. I assumed the beams were twice as high as they were wide (1:1.5 or so might be more the ratio artist's sketch suggests in the manual). Of course, I could adjust the beam depth or possibly try turning the beams on their sides. However, when I do that (and thereby increase the beam width) then there's the difficulty of the major members blocking the hull apertures (windows, shuttle bays, lifeboat hatches, etc).
I might dig up my old steels or reinforced concrete textbooks from college to see if I can come up with a somewhat sensible interpretation of the frame. The performance specs in the tech manual (the gravitational accelerations) could come in handy to figure that out...
Of course, I can also just forget it, invent something that looks right and say the beams are just amazingly strong - you know - like transparent aluminum or something.