Your kit GFCI's may have been installed by someone who didn't know any better. Sometimes I put multiple GFCI's in the kit to keep the refrigerator off a protected circuit.
Kit counter top circuits are for kitchen counter top receps only. You can run your bathroom circuit thru the kitchen if that is what you are asking.
As far as the wiring run outside, it is always a good idea to protect it. Tne definitions of "outside" will vary. IMO, if you are in the floor joist chase, you are still inside.