Too simple.
You've taken the role of synchros out of the equation (or, more accuratly, you've assumed they are not able to handle increased inertia.)
My transmission was rated to handle 550ftlbs at the input shaft. Is it capable of handling additional torque? Yup. Does additional torque put additional strain on the transmission? Yup. Does it function differently? Nope.
The syncro's can handle it sure, but they have to handle things differently with different input load to slow down.
They design the trans to slow down xyz weight with an abc size/style/etc synco. Now you have more weight, So, maybe the design needs to be changed. I suppose tho, the higher RPM's with a smaller clutch in a gasser operation would negate this to a point?
Maybe this analogy can be applied some how. Braking system.
Brakes are designed to stop the truck well from 108mph. I suppose this pertains to the gassers, cuz now we can run the trucks to 145+. Will the OEM brakes work? Yeah, Will they slow the truck down at the same rate? No. Redesign the brakes for the application.
My main argument here is that I can no longer do the 2nd to 3rd shift worth a damn if I'm over 2500rpm. 3-4th and so on is "ok" but I tend to grind gears even with fully depressing the clutch, with upgrade hydrolics with the master shaft about 1/2 the width of a 1/2" nut. So I'm pressing the clutch further then stock. (take a nut, grind 1/2 it down, and use it as a stopper to prevent the shaft from turn on the eye-hook)
Yeah, I have more HP, however, I have a lagger turbo then stock, so there for I have less HP in 2nd gear then I did with the stock turbo, there for, that gear will accelerate slower.
However, I do recall that my ConFE did shift slower then my stocker. So I'm leaning toward the material if anything.