In my opinion and I think UGS as well to be parametric and associative holes should be attached to edges of solid or if this is not possible they should be attached to datum planes that are attached to edges or faces of solid model. Position of holes should be fully specified. This is a practice...
if you use more than one primitive then they are not associated to each other. If you change one primitive parameters then the other primitives are not going to move with this change and they should be moved manually. But you are using holes. Holes are form features not primitives. may be if you...
I usually do not use the alternate thickness because I have not used the offset faces yet. I though if you hollow all the same thickness it might work. It is possible that hollow (offset) faces are moving in different directions and software can not connect them together.
1.top flange is in bending and axial because there is uniform pressure applied to it (load).
2. top flange and bottom flange should not have uniform stress across the thickness because the outer fibers of each flange will see the maximum stress.