Braces can do bad things to a frame, in theory. The provide apparent stiffness at low forces, but cause havoc on column bending (and bearing forces, as you've seen) at high loads. It's usually a trad off between bigger columns and smaller beams, in my experience.
Will the model survive without the braces?
In my models, braces get full loads, since they will actully see nearly full loads (any load added after the tenon makes contact with the housing). I try to have the framer avoid them when possible.
Remember that (1) very few structures are made with lumber which is of minimum size and grade strength and (2) very few have actually withstood full environmental loads. The change of 85psf ground load is just 2% per year. How many houses by the TF have been in service for more than 50 years? Of those, how many were designed with minimally sized members. Now that your answer is close to, or exactly zero, can you really extrapolate success from such a small sample?
As engineers, we design to save lives, not necessarily to minimize cost or promulagate tradition. If youre analysis is good, then the forces are real. I have worked on both architectual, consumer-ish, and space flight hardware, and have had the opportunity to model strucutres which I subsequently broke or had stress monitors on in a test environment - the forces you are seeing are real.
