I use a similar item along with something called an ursack which is lighter and adapts to packing better (although less bear resistant than the hard shell containers.  On a thread discussing time to portage, the external frame pack issue came up.  I use an external frame pack because it is better able to help me carry a load.  I also like that it had two large main compartments that would come in handy in your situation.  I see no problem with packing your gear you want to keep odor free in one compartment (presumably protected in something waterproof) and you smelly stuiff in another.  The pack may have some smells but I would not worry about a bear messing with it if it was left out empty (I would not bring it into the tent).