As I understand what the FEM models reveal, it means that through adding stiffeners the structure finds (and needs to meet) the kind of deformation shown because the energy of deformation is such way minimum, i.e., the lower energy of deformation available within the restraints, loadings, and actual configuration present in every separate case.
Perhaps the first pair is easier to understand; when adding the stiffeners, with the pair of forces applied as a torque, this torque is efficiently transmitted to the whole section, that then, trough the stouter open box-like short segments passes efficiently the torque to the following and so on. In the case when there are no inner stiffeners, you have basically in each flange one force to be resisted by the respective flange, and the mechanism is less a torsional one than two separate bendings. The fact that the FEM program shows be the case *** should *** mean that for the loading that I have imparted in the way I have imparted it, it finds to have less energy of deformation taking the load in that bending way than resourcing to some other (theoretical) more torsional in behaviour output.
The contrary is the case, relatively, when we add the stiffeners: now each flange cannot work as separately to meet its own lateral load through bending in the flange plane, and lamentably for a maxwellian daemon that would love to keep the former mechanism, the presence of the stiffeners ensure and forces that the torsional mode, and not one where the flanges bend in their respective plane, prevails. So we have forced through our stiffeners the structure to go for some particular way of deformation, which, again, since the solution of the model in FEM, should be the one having less energy of deformation to meet the loads as it is.
We could model now stiffeners less and less thick; at one given moment their addition would be irrelevant when compared to the overall stiffness of the beam itself, and then the model would revert to the situation where bending in each flange is predominant.
More, these are elastic models. Imagine that by whatever the reason we lose the stiffeners or separate them softly, then, I agree with you, the overal section is there and no less than what it provides is to be expected from it (rolling secondary stresses etc being ignored etc). When looking at these results, that fortunately mostly remain under the yield stress of the material, we must not forget that when dealing with a strength case we could account with some plasticity that also would show at least the minimum strength that you expect of the overall bare beam. So having some particular zones with a bigger stress when the analysis and material are in the model just elastic may well not reveal the final strength issues; making the model with elasto-plastic material when the forces engage some plastic regions would again show that you are right (again, residual stresses etc apart) in expecting no less than the basic beam provides.
But as long as the model is right (on which I am open to any contrary illustration) and the program as well, it leads you to ascertain that having stiffeners quite likely in the service levels will make the beam enter a more torsional response and then as per the op question, this is not precisely what one would be trying to do.