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.
you should be able to use assemblies->deform part in your assembly to modify a standard part without getting a new number. This way the part in library will not change but it will be shown at a different shape (length for example) in your assembly. look at help documentation for how to use...
If you just mesh one surface of the part yes it will go thru the part but if you use the midsurface feature and mesh all surfaces of the midsurface feature or use solid elements for the entire part it will not do that.